Sat Apr 15 10:17:44 UTC 2023  I: starting to build mdtraj/bookworm/arm64 on jenkins on '2023-04-15 10:17'
Sat Apr 15 10:17:44 UTC 2023  I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_29/19322/console.log
Sat Apr 15 10:17:44 UTC 2023  I: Downloading source for bookworm/mdtraj=1.9.7-6
--2023-04-15 10:17:45--  http://cdn-fastly.deb.debian.org/debian/pool/main/m/mdtraj/mdtraj_1.9.7-6.dsc
Connecting to 78.137.99.97:3128... connected.
Proxy request sent, awaiting response... 200 OK
Length: 2626 (2.6K) [text/prs.lines.tag]
Saving to: ‘mdtraj_1.9.7-6.dsc’

     0K ..                                                    100%  140M=0s

2023-04-15 10:17:45 (140 MB/s) - ‘mdtraj_1.9.7-6.dsc’ saved [2626/2626]

Sat Apr 15 10:17:45 UTC 2023  I: mdtraj_1.9.7-6.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: 1.9.7-6
Maintainer: Debichem Team <debichem-devel@lists.alioth.debian.org>
Uploaders: Drew Parsons <dparsons@debian.org>
Homepage: http://mdtraj.org/
Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/debichem-team/mdtraj
Vcs-Git: https://salsa.debian.org/debichem-team/mdtraj.git
Testsuite: autopkgtest
Testsuite-Triggers: python3-ipykernel, python3-jupyter-client, python3-matplotlib, python3-nbformat, python3-pandas, python3-pytest, python3-six, python3-sklearn
Build-Depends: debhelper-compat (= 13), dh-python, cython3 (>= 0.29~), python3-setuptools, python3-all-dev, python3-numpy (>= 1.6~), python3-scipy, python3-astunparse, python3-networkx, python3-pandas, python3-pyparsing, python3-sphinx, python3-tables, libjs-mathjax
Build-Depends-Indep: python3-msmb-theme, python3-ipykernel, python3-jupyter-client, python3-matplotlib, python3-nbconvert, python3-nbformat, python3-numpydoc, python3-six, python3-sklearn
Package-List:
 python-mdtraj-doc deb doc optional arch=all
 python3-mdtraj deb python optional arch=any-amd64,arm64,i386
Checksums-Sha1:
 8796d6d806be9d9c3f4051e3a6f52b6130a1c872 21660511 mdtraj_1.9.7.orig.tar.gz
 5f5c48fd38cf995f9668b469bbd17934c0c2f83a 299396 mdtraj_1.9.7-6.debian.tar.xz
Checksums-Sha256:
 5c84c41e3a01e6512ac7077d153c8cb1ee01d82140ca532507c50c87650937e6 21660511 mdtraj_1.9.7.orig.tar.gz
 8b1fa5b9825164ad10551e7cb187046044c96d208815cad08c971443cf0e5748 299396 mdtraj_1.9.7-6.debian.tar.xz
Files:
 2e96eaa720282ebf2eff54001225d68a 21660511 mdtraj_1.9.7.orig.tar.gz
 259f3ebb6b17c60b7fe6a0af121ebd6b 299396 mdtraj_1.9.7-6.debian.tar.xz

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Sat Apr 15 10:17:45 UTC 2023  I: Checking whether the package is not for us
Sat Apr 15 10:17:45 UTC 2023  I: Starting 1st build on remote node codethink16-arm64.debian.net.
Sat Apr 15 10:17:45 UTC 2023  I: Preparing to do remote build '1' on codethink16-arm64.debian.net.
Sat Apr 15 10:47:45 UTC 2023  I: Deleting $TMPDIR on codethink16-arm64.debian.net.
I: pbuilder: network access will be disabled during build
I: Current time: Fri Apr 14 22:18:41 -12 2023
I: pbuilder-time-stamp: 1681553921
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz]
I: copying local configuration
W: --override-config is not set; not updating apt.conf Read the manpage for details.
I: mounting /proc filesystem
I: mounting /sys filesystem
I: creating /{dev,run}/shm
I: mounting /dev/pts filesystem
I: redirecting /dev/ptmx to /dev/pts/ptmx
I: policy-rc.d already exists
I: Copying source file
I: copying [mdtraj_1.9.7-6.dsc]
I: copying [./mdtraj_1.9.7.orig.tar.gz]
I: copying [./mdtraj_1.9.7-6.debian.tar.xz]
I: Extracting source
gpgv: Signature made Tue Feb 28 22:55:59 2023 -12
gpgv:                using RSA key 23C9A93E585819E9126D0A36573EF1E4BD5A01FA
gpgv:                issuer "dparsons@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./mdtraj_1.9.7-6.dsc: no acceptable signature found
dpkg-source: info: extracting mdtraj in mdtraj-1.9.7
dpkg-source: info: unpacking mdtraj_1.9.7.orig.tar.gz
dpkg-source: info: unpacking mdtraj_1.9.7-6.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying docs_use_local_mathjax.patch
dpkg-source: info: applying build_dir_pybuild.patch
dpkg-source: info: applying python_hashbang.patch
dpkg-source: info: applying test_gsd_skip.patch
dpkg-source: info: applying check_sse2.patch
dpkg-source: info: applying 32bit_skip_image_molecule.patch
dpkg-source: info: applying test_relax_tol.patch
dpkg-source: info: applying rename-mdconvert-mdtraj.patch
dpkg-source: info: applying drop_notebook_in_docs.patch
dpkg-source: info: applying test_increase_timeout.patch
dpkg-source: info: applying python3.11_PR1758.patch
I: using fakeroot in build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/20111/tmp/hooks/D02_print_environment starting
I: set
  BUILDDIR='/build'
  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=8'
  DISTRIBUTION='bookworm'
  HOME='/var/lib/jenkins'
  HOST_ARCH='arm64'
  IFS=' 	
  '
  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='20111'
  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.qrvXaQUi/pbuilderrc_Z7ke --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.qrvXaQUi/b1 --logfile b1/build.log mdtraj_1.9.7-6.dsc'
  SUDO_GID='117'
  SUDO_UID='110'
  SUDO_USER='jenkins'
  TERM='unknown'
  TZ='/usr/share/zoneinfo/Etc/GMT+12'
  USER='root'
  USERNAME='root'
  _='/usr/bin/systemd-run'
  http_proxy='http://192.168.101.16:3128'
I: uname -a
  Linux codethink16-arm64 4.15.0-208-generic #220-Ubuntu SMP Mon Mar 20 14:28:12 UTC 2023 aarch64 GNU/Linux
I: ls -l /bin
  lrwxrwxrwx 1 root root 7 Apr 14 00:48 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/20111/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-python, cython3 (>= 0.29~), python3-setuptools, python3-all-dev, python3-numpy (>= 1.6~), python3-scipy, python3-astunparse, python3-networkx, python3-pandas, python3-pyparsing, python3-sphinx, python3-tables, libjs-mathjax, python3-msmb-theme, python3-ipykernel, python3-jupyter-client, python3-matplotlib, python3-nbconvert, python3-nbformat, python3-numpydoc, python3-six, python3-sklearn
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19616 files and directories currently installed.)
Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ...
Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ...
dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested:
 pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however:
  Package debhelper-compat is not installed.
 pbuilder-satisfydepends-dummy depends on dh-python; however:
  Package dh-python is not installed.
 pbuilder-satisfydepends-dummy depends on cython3 (>= 0.29~); however:
  Package cython3 is not installed.
 pbuilder-satisfydepends-dummy depends on python3-setuptools; however:
  Package python3-setuptools is not installed.
 pbuilder-satisfydepends-dummy depends on python3-all-dev; however:
  Package python3-all-dev is not installed.
 pbuilder-satisfydepends-dummy depends on python3-numpy (>= 1.6~); however:
  Package python3-numpy is not installed.
 pbuilder-satisfydepends-dummy depends on python3-scipy; however:
  Package python3-scipy is not installed.
 pbuilder-satisfydepends-dummy depends on python3-astunparse; however:
  Package python3-astunparse is not installed.
 pbuilder-satisfydepends-dummy depends on python3-networkx; however:
  Package python3-networkx is not installed.
 pbuilder-satisfydepends-dummy depends on python3-pandas; however:
  Package python3-pandas is not installed.
 pbuilder-satisfydepends-dummy depends on python3-pyparsing; however:
  Package python3-pyparsing is not installed.
 pbuilder-satisfydepends-dummy depends on python3-sphinx; however:
  Package python3-sphinx is not installed.
 pbuilder-satisfydepends-dummy depends on python3-tables; however:
  Package python3-tables is not installed.
 pbuilder-satisfydepends-dummy depends on libjs-mathjax; however:
  Package libjs-mathjax is not installed.
 pbuilder-satisfydepends-dummy depends on python3-msmb-theme; however:
  Package python3-msmb-theme is not installed.
 pbuilder-satisfydepends-dummy depends on python3-ipykernel; however:
  Package python3-ipykernel is not installed.
 pbuilder-satisfydepends-dummy depends on python3-jupyter-client; however:
  Package python3-jupyter-client is not installed.
 pbuilder-satisfydepends-dummy depends on python3-matplotlib; however:
  Package python3-matplotlib is not installed.
 pbuilder-satisfydepends-dummy depends on python3-nbconvert; however:
  Package python3-nbconvert is not installed.
 pbuilder-satisfydepends-dummy depends on python3-nbformat; however:
  Package python3-nbformat is not installed.
 pbuilder-satisfydepends-dummy depends on python3-numpydoc; however:
  Package python3-numpydoc is not installed.
 pbuilder-satisfydepends-dummy depends on python3-six; however:
  Package python3-six is not installed.
 pbuilder-satisfydepends-dummy depends on python3-sklearn; however:
  Package python3-sklearn is not installed.

Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ...
Reading package lists...
Building dependency tree...
Reading state information...
Initializing package states...
Writing extended state information...
Building tag database...
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
The following NEW packages will be installed:
  autoconf{a} automake{a} autopoint{a} autotools-dev{a} blt{a} bsdextrautils{a} ca-certificates{a} cython3{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} docutils-common{a} dwz{a} file{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-font-awesome{a} fonts-lato{a} fonts-lyx{a} fonts-mathjax{a} gdb{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libaec0{a} libarchive-zip-perl{a} libbabeltrace1{a} libblas3{a} libblosc1{a} libboost-dev{a} libboost-regex1.74.0{a} libboost1.74-dev{a} libbrotli1{a} libbsd0{a} libcurl3-gnutls{a} libcurl4{a} libdebhelper-perl{a} libdebuginfod-common{a} libdebuginfod1{a} libdeflate0{a} libdw1{a} libelf1{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgfortran5{a} libglib2.0-0{a} libgraphite2-3{a} libharfbuzz0b{a} libhdf5-103-1{a} libicu72{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-jquery-ui{a} libjs-mathjax{a} libjs-sphinxdoc{a} libjs-underscore{a} libjson-perl{a} liblapack3{a} liblbfgsb0{a} liblcms2-2{a} libldap-2.5-0{a} liblerc4{a} liblzo2-2{a} libmagic-mgc{a} libmagic1{a} libnghttp2-14{a} libnorm1{a} libopenblas-dev{a} libopenblas-pthread-dev{a} libopenblas0{a} libopenblas0-pthread{a} libopenjp2-7{a} libpgm-5.3-0{a} libpipeline1{a} libpng16-16{a} libproc2-0{a} libpsl5{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.11{a} libpython3.11-dev{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libqhull-r8.0{a} libraqm0{a} libreadline8{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsnappy1v5{a} libsodium23{a} libsource-highlight-common{a} libsource-highlight4v5{a} libssh2-1{a} libsub-override-perl{a} libsz2{a} libtcl8.6{a} libtiff6{a} libtk8.6{a} libtool{a} libuchardet0{a} libwebp7{a} libwebpdemux2{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxft2{a} libxml2{a} libxrender1{a} libxsimd-dev{a} libxslt1.1{a} libxss1{a} libzmq5{a} m4{a} man-db{a} media-types{a} openssl{a} po-debconf{a} procps{a} python-babel-localedata{a} python-matplotlib-data{a} python-tables-data{a} python-tinycss2-common{a} python3{a} python3-alabaster{a} python3-all{a} python3-all-dev{a} python3-appdirs{a} python3-asttokens{a} python3-astunparse{a} python3-attr{a} python3-babel{a} python3-backcall{a} python3-beniget{a} python3-bleach{a} python3-brotli{a} python3-bs4{a} python3-bytecode{a} python3-certifi{a} python3-cffi-backend{a} python3-chardet{a} python3-charset-normalizer{a} python3-contourpy{a} python3-coverage{a} python3-cycler{a} python3-dateutil{a} python3-debugpy{a} python3-decorator{a} python3-defusedxml{a} python3-dev{a} python3-distutils{a} python3-docutils{a} python3-entrypoints{a} python3-executing{a} python3-fastjsonschema{a} python3-fonttools{a} python3-fs{a} python3-gast{a} python3-html5lib{a} python3-idna{a} python3-imagesize{a} python3-ipykernel{a} python3-ipython{a} python3-jedi{a} python3-jinja2{a} python3-joblib{a} python3-jsonschema{a} python3-jupyter-client{a} python3-jupyter-core{a} python3-jupyterlab-pygments{a} python3-kiwisolver{a} python3-lib2to3{a} python3-lxml{a} python3-lz4{a} python3-markupsafe{a} python3-matplotlib{a} python3-matplotlib-inline{a} python3-minimal{a} python3-mpmath{a} python3-msmb-theme{a} python3-nbclient{a} python3-nbconvert{a} python3-nbformat{a} python3-nest-asyncio{a} python3-networkx{a} python3-numexpr{a} python3-numpy{a} python3-numpydoc{a} python3-packaging{a} python3-pandas{a} python3-pandas-lib{a} python3-pandocfilters{a} python3-parso{a} python3-pexpect{a} python3-pickleshare{a} python3-pil{a} python3-pil.imagetk{a} python3-pkg-resources{a} python3-ply{a} python3-prompt-toolkit{a} python3-psutil{a} python3-ptyprocess{a} python3-pure-eval{a} python3-py{a} python3-pydevd{a} python3-pygments{a} python3-pyparsing{a} python3-pyrsistent{a} python3-pythran{a} python3-requests{a} python3-roman{a} python3-scipy{a} python3-setuptools{a} python3-six{a} python3-sklearn{a} python3-sklearn-lib{a} python3-snowballstemmer{a} python3-soupsieve{a} python3-sphinx{a} python3-sphinx-rtd-theme{a} python3-stack-data{a} python3-sympy{a} python3-tables{a} python3-tables-lib{a} python3-threadpoolctl{a} python3-tinycss2{a} python3-tk{a} python3-tornado{a} python3-traitlets{a} python3-tz{a} python3-ufolib2{a} python3-urllib3{a} python3-wcwidth{a} python3-webencodings{a} python3-zmq{a} python3.11{a} python3.11-dev{a} python3.11-minimal{a} readline-common{a} sensible-utils{a} sgml-base{a} sphinx-common{a} sphinx-rtd-theme-common{a} tk8.6-blt2.5{a} ucf{a} unicode-data{a} x11-common{a} xml-core{a} zlib1g-dev{a} 
The following packages are RECOMMENDED but will NOT be installed:
  curl isympy-common javascript-common libarchive-cpio-perl libc6-dbg libglib2.0-data libjson-xs-perl libldap-common libltdl-dev libmail-sendmail-perl libpaper-utils libsasl2-modules lynx pandoc psmisc publicsuffix python3-bottleneck python3-gdal python3-json-pointer python3-nose python3-odf python3-olefile python3-openpyxl python3-pydot python3-pygraphviz python3-pytest python3-rfc3987 python3-simplejson python3-uritemplate python3-webcolors python3-yaml shared-mime-info wget xdg-user-dirs 
0 packages upgraded, 262 newly installed, 0 to remove and 0 not upgraded.
Need to get 161 MB of archives. After unpacking 864 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian bookworm/main arm64 fonts-lato all 2.0-2.1 [2696 kB]
Get: 2 http://deb.debian.org/debian bookworm/main arm64 sensible-utils all 0.0.17+nmu1 [19.0 kB]
Get: 3 http://deb.debian.org/debian bookworm/main arm64 ucf all 3.0043+nmu1 [55.2 kB]
Get: 4 http://deb.debian.org/debian bookworm/main arm64 libdebuginfod-common all 0.188-2.1 [21.5 kB]
Get: 5 http://deb.debian.org/debian bookworm/main arm64 libpython3.11-minimal arm64 3.11.2-6 [806 kB]
Get: 6 http://deb.debian.org/debian bookworm/main arm64 libexpat1 arm64 2.5.0-1 [84.8 kB]
Get: 7 http://deb.debian.org/debian bookworm/main arm64 python3.11-minimal arm64 3.11.2-6 [1858 kB]
Get: 8 http://deb.debian.org/debian bookworm/main arm64 python3-minimal arm64 3.11.2-1+b1 [26.3 kB]
Get: 9 http://deb.debian.org/debian bookworm/main arm64 media-types all 10.0.0 [26.1 kB]
Get: 10 http://deb.debian.org/debian bookworm/main arm64 readline-common all 8.2-1.3 [69.0 kB]
Get: 11 http://deb.debian.org/debian bookworm/main arm64 libreadline8 arm64 8.2-1.3 [155 kB]
Get: 12 http://deb.debian.org/debian bookworm/main arm64 libpython3.11-stdlib arm64 3.11.2-6 [1747 kB]
Get: 13 http://deb.debian.org/debian bookworm/main arm64 python3.11 arm64 3.11.2-6 [572 kB]
Get: 14 http://deb.debian.org/debian bookworm/main arm64 libpython3-stdlib arm64 3.11.2-1+b1 [9296 B]
Get: 15 http://deb.debian.org/debian bookworm/main arm64 python3 arm64 3.11.2-1+b1 [26.3 kB]
Get: 16 http://deb.debian.org/debian bookworm/main arm64 sgml-base all 1.31 [15.4 kB]
Get: 17 http://deb.debian.org/debian bookworm/main arm64 libproc2-0 arm64 2:4.0.2-3 [60.1 kB]
Get: 18 http://deb.debian.org/debian bookworm/main arm64 procps arm64 2:4.0.2-3 [698 kB]
Get: 19 http://deb.debian.org/debian bookworm/main arm64 openssl arm64 3.0.8-1 [1373 kB]
Get: 20 http://deb.debian.org/debian bookworm/main arm64 ca-certificates all 20230311 [153 kB]
Get: 21 http://deb.debian.org/debian bookworm/main arm64 libmagic-mgc arm64 1:5.44-3 [305 kB]
Get: 22 http://deb.debian.org/debian bookworm/main arm64 libmagic1 arm64 1:5.44-3 [98.5 kB]
Get: 23 http://deb.debian.org/debian bookworm/main arm64 file arm64 1:5.44-3 [42.5 kB]
Get: 24 http://deb.debian.org/debian bookworm/main arm64 gettext-base arm64 0.21-12 [159 kB]
Get: 25 http://deb.debian.org/debian bookworm/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB]
Get: 26 http://deb.debian.org/debian bookworm/main arm64 groff-base arm64 1.22.4-10 [861 kB]
Get: 27 http://deb.debian.org/debian bookworm/main arm64 bsdextrautils arm64 2.38.1-5+b1 [86.9 kB]
Get: 28 http://deb.debian.org/debian bookworm/main arm64 libpipeline1 arm64 1.5.7-1 [36.4 kB]
Get: 29 http://deb.debian.org/debian bookworm/main arm64 man-db arm64 2.11.2-2 [1369 kB]
Get: 30 http://deb.debian.org/debian bookworm/main arm64 m4 arm64 1.4.19-3 [276 kB]
Get: 31 http://deb.debian.org/debian bookworm/main arm64 autoconf all 2.71-3 [332 kB]
Get: 32 http://deb.debian.org/debian bookworm/main arm64 autotools-dev all 20220109.1 [51.6 kB]
Get: 33 http://deb.debian.org/debian bookworm/main arm64 automake all 1:1.16.5-1.3 [823 kB]
Get: 34 http://deb.debian.org/debian bookworm/main arm64 autopoint all 0.21-12 [495 kB]
Get: 35 http://deb.debian.org/debian bookworm/main arm64 libtcl8.6 arm64 8.6.13+dfsg-2 [973 kB]
Get: 36 http://deb.debian.org/debian bookworm/main arm64 libbrotli1 arm64 1.0.9-2+b6 [269 kB]
Get: 37 http://deb.debian.org/debian bookworm/main arm64 libpng16-16 arm64 1.6.39-2 [269 kB]
Get: 38 http://deb.debian.org/debian bookworm/main arm64 libfreetype6 arm64 2.12.1+dfsg-4 [369 kB]
Get: 39 http://deb.debian.org/debian bookworm/main arm64 fonts-dejavu-core all 2.37-6 [1068 kB]
Get: 40 http://deb.debian.org/debian bookworm/main arm64 fontconfig-config arm64 2.14.1-4 [315 kB]
Get: 41 http://deb.debian.org/debian bookworm/main arm64 libfontconfig1 arm64 2.14.1-4 [381 kB]
Get: 42 http://deb.debian.org/debian bookworm/main arm64 libxau6 arm64 1:1.0.9-1 [19.7 kB]
Get: 43 http://deb.debian.org/debian bookworm/main arm64 libbsd0 arm64 0.11.7-2 [115 kB]
Get: 44 http://deb.debian.org/debian bookworm/main arm64 libxdmcp6 arm64 1:1.1.2-3 [25.4 kB]
Get: 45 http://deb.debian.org/debian bookworm/main arm64 libxcb1 arm64 1.15-1 [143 kB]
Get: 46 http://deb.debian.org/debian bookworm/main arm64 libx11-data all 2:1.8.4-2 [292 kB]
Get: 47 http://deb.debian.org/debian bookworm/main arm64 libx11-6 arm64 2:1.8.4-2 [736 kB]
Get: 48 http://deb.debian.org/debian bookworm/main arm64 libxrender1 arm64 1:0.9.10-1.1 [32.0 kB]
Get: 49 http://deb.debian.org/debian bookworm/main arm64 libxft2 arm64 2.3.6-1 [58.7 kB]
Get: 50 http://deb.debian.org/debian bookworm/main arm64 libxext6 arm64 2:1.3.4-1+b1 [51.7 kB]
Get: 51 http://deb.debian.org/debian bookworm/main arm64 x11-common all 1:7.7+23 [252 kB]
Get: 52 http://deb.debian.org/debian bookworm/main arm64 libxss1 arm64 1:1.2.3-1 [17.8 kB]
Get: 53 http://deb.debian.org/debian bookworm/main arm64 libtk8.6 arm64 8.6.13-2 [729 kB]
Get: 54 http://deb.debian.org/debian bookworm/main arm64 tk8.6-blt2.5 arm64 2.5.3+dfsg-4.1 [540 kB]
Get: 55 http://deb.debian.org/debian bookworm/main arm64 blt arm64 2.5.3+dfsg-4.1 [14.9 kB]
Get: 56 http://deb.debian.org/debian bookworm/main arm64 cython3 arm64 0.29.32-2+b1 [1223 kB]
Get: 57 http://deb.debian.org/debian bookworm/main arm64 libdebhelper-perl all 13.11.4 [81.2 kB]
Get: 58 http://deb.debian.org/debian bookworm/main arm64 libtool all 2.4.7-5 [517 kB]
Get: 59 http://deb.debian.org/debian bookworm/main arm64 dh-autoreconf all 20 [17.1 kB]
Get: 60 http://deb.debian.org/debian bookworm/main arm64 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 61 http://deb.debian.org/debian bookworm/main arm64 libsub-override-perl all 0.09-4 [9304 B]
Get: 62 http://deb.debian.org/debian bookworm/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB]
Get: 63 http://deb.debian.org/debian bookworm/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B]
Get: 64 http://deb.debian.org/debian bookworm/main arm64 libelf1 arm64 0.188-2.1 [173 kB]
Get: 65 http://deb.debian.org/debian bookworm/main arm64 dwz arm64 0.15-1 [101 kB]
Get: 66 http://deb.debian.org/debian bookworm/main arm64 libicu72 arm64 72.1-3 [9204 kB]
Get: 67 http://deb.debian.org/debian bookworm/main arm64 libxml2 arm64 2.9.14+dfsg-1.1+b3 [619 kB]
Get: 68 http://deb.debian.org/debian bookworm/main arm64 gettext arm64 0.21-12 [1248 kB]
Get: 69 http://deb.debian.org/debian bookworm/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 70 http://deb.debian.org/debian bookworm/main arm64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 71 http://deb.debian.org/debian bookworm/main arm64 debhelper all 13.11.4 [942 kB]
Get: 72 http://deb.debian.org/debian bookworm/main arm64 python3-lib2to3 all 3.11.2-2 [76.2 kB]
Get: 73 http://deb.debian.org/debian bookworm/main arm64 python3-distutils all 3.11.2-2 [131 kB]
Get: 74 http://deb.debian.org/debian bookworm/main arm64 dh-python all 5.20230130 [104 kB]
Get: 75 http://deb.debian.org/debian bookworm/main arm64 xml-core all 0.18+nmu1 [23.8 kB]
Get: 76 http://deb.debian.org/debian bookworm/main arm64 docutils-common all 0.19+dfsg-6 [127 kB]
Get: 77 http://deb.debian.org/debian bookworm/main arm64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [517 kB]
Get: 78 http://deb.debian.org/debian bookworm/main arm64 fonts-lyx all 2.3.7-1 [186 kB]
Get: 79 http://deb.debian.org/debian bookworm/main arm64 fonts-mathjax all 2.7.9+dfsg-1 [2210 kB]
Get: 80 http://deb.debian.org/debian bookworm/main arm64 libdw1 arm64 0.188-2.1 [219 kB]
Get: 81 http://deb.debian.org/debian bookworm/main arm64 libglib2.0-0 arm64 2.74.6-1 [1311 kB]
Get: 82 http://deb.debian.org/debian bookworm/main arm64 libbabeltrace1 arm64 1.5.11-1+b2 [158 kB]
Get: 83 http://deb.debian.org/debian bookworm/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg-10 [20.8 kB]
Get: 84 http://deb.debian.org/debian bookworm/main arm64 libsasl2-2 arm64 2.1.28+dfsg-10 [58.0 kB]
Get: 85 http://deb.debian.org/debian bookworm/main arm64 libldap-2.5-0 arm64 2.5.13+dfsg-5 [171 kB]
Get: 86 http://deb.debian.org/debian bookworm/main arm64 libnghttp2-14 arm64 1.52.0-1 [67.9 kB]
Get: 87 http://deb.debian.org/debian bookworm/main arm64 libpsl5 arm64 0.21.2-1 [58.6 kB]
Get: 88 http://deb.debian.org/debian bookworm/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b2 [59.4 kB]
Get: 89 http://deb.debian.org/debian bookworm/main arm64 libssh2-1 arm64 1.10.0-3+b1 [172 kB]
Get: 90 http://deb.debian.org/debian bookworm/main arm64 libcurl3-gnutls arm64 7.88.1-8 [357 kB]
Get: 91 http://deb.debian.org/debian bookworm/main arm64 libdebuginfod1 arm64 0.188-2.1 [26.4 kB]
Get: 92 http://deb.debian.org/debian bookworm/main arm64 libpython3.11 arm64 3.11.2-6 [1841 kB]
Get: 93 http://deb.debian.org/debian bookworm/main arm64 libsource-highlight-common all 3.1.9-4.2 [77.4 kB]
Get: 94 http://deb.debian.org/debian bookworm/main arm64 libboost-regex1.74.0 arm64 1.74.0+ds1-20 [448 kB]
Get: 95 http://deb.debian.org/debian bookworm/main arm64 libsource-highlight4v5 arm64 3.1.9-4.2+b3 [229 kB]
Get: 96 http://deb.debian.org/debian bookworm/main arm64 gdb arm64 13.1-2 [3677 kB]
Get: 97 http://deb.debian.org/debian bookworm/main arm64 libaec0 arm64 1.0.6-1+b1 [19.9 kB]
Get: 98 http://deb.debian.org/debian bookworm/main arm64 libblas3 arm64 3.11.0-2 [91.4 kB]
Get: 99 http://deb.debian.org/debian bookworm/main arm64 libsnappy1v5 arm64 1.1.9-3 [25.4 kB]
Get: 100 http://deb.debian.org/debian bookworm/main arm64 libblosc1 arm64 1.21.3+ds-1 [38.6 kB]
Get: 101 http://deb.debian.org/debian bookworm/main arm64 libboost1.74-dev arm64 1.74.0+ds1-20 [9510 kB]
Get: 102 http://deb.debian.org/debian bookworm/main arm64 libboost-dev arm64 1.74.0.3 [4548 B]
Get: 103 http://deb.debian.org/debian bookworm/main arm64 libcurl4 arm64 7.88.1-8 [361 kB]
Get: 104 http://deb.debian.org/debian bookworm/main arm64 libdeflate0 arm64 1.14-1 [54.3 kB]
Get: 105 http://deb.debian.org/debian bookworm/main arm64 libexpat1-dev arm64 2.5.0-1 [135 kB]
Get: 106 http://deb.debian.org/debian bookworm/main arm64 libfribidi0 arm64 1.0.8-2.1 [64.9 kB]
Get: 107 http://deb.debian.org/debian bookworm/main arm64 libgfortran5 arm64 12.2.0-14 [340 kB]
Get: 108 http://deb.debian.org/debian bookworm/main arm64 libgraphite2-3 arm64 1.3.14-1 [75.6 kB]
Get: 109 http://deb.debian.org/debian bookworm/main arm64 libharfbuzz0b arm64 6.0.0+dfsg-3 [1914 kB]
Get: 110 http://deb.debian.org/debian bookworm/main arm64 libsz2 arm64 1.0.6-1+b1 [7740 B]
Get: 111 http://deb.debian.org/debian bookworm/main arm64 libhdf5-103-1 arm64 1.10.8+repack1-1 [1037 kB]
Get: 112 http://deb.debian.org/debian bookworm/main arm64 libimagequant0 arm64 2.17.0-1 [31.3 kB]
Get: 113 http://deb.debian.org/debian bookworm/main arm64 libjbig0 arm64 2.1-6.1 [30.0 kB]
Get: 114 http://deb.debian.org/debian bookworm/main arm64 libjpeg62-turbo arm64 1:2.1.5-2 [171 kB]
Get: 115 http://deb.debian.org/debian bookworm/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB]
Get: 116 http://deb.debian.org/debian bookworm/main arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB]
Get: 117 http://deb.debian.org/debian bookworm/main arm64 libjs-mathjax all 2.7.9+dfsg-1 [5667 kB]
Get: 118 http://deb.debian.org/debian bookworm/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB]
Get: 119 http://deb.debian.org/debian bookworm/main arm64 libjs-sphinxdoc all 5.3.0-4 [130 kB]
Get: 120 http://deb.debian.org/debian bookworm/main arm64 libjson-perl all 4.10000-1 [87.5 kB]
Get: 121 http://deb.debian.org/debian bookworm/main arm64 libopenblas0-pthread arm64 0.3.21+ds-4 [4532 kB]
Get: 122 http://deb.debian.org/debian bookworm/main arm64 liblapack3 arm64 3.11.0-2 [1664 kB]
Get: 123 http://deb.debian.org/debian bookworm/main arm64 liblbfgsb0 arm64 3.0+dfsg.4-1 [24.9 kB]
Get: 124 http://deb.debian.org/debian bookworm/main arm64 liblcms2-2 arm64 2.14-2 [143 kB]
Get: 125 http://deb.debian.org/debian bookworm/main arm64 liblerc4 arm64 4.0.0+ds-2 [138 kB]
Get: 126 http://deb.debian.org/debian bookworm/main arm64 liblzo2-2 arm64 2.10-2 [51.8 kB]
Get: 127 http://deb.debian.org/debian bookworm/main arm64 libnorm1 arm64 1.5.9+dfsg-2 [202 kB]
Get: 128 http://deb.debian.org/debian bookworm/main arm64 libopenblas0 arm64 0.3.21+ds-4 [32.6 kB]
Get: 129 http://deb.debian.org/debian bookworm/main arm64 libopenblas-pthread-dev arm64 0.3.21+ds-4 [3169 kB]
Get: 130 http://deb.debian.org/debian bookworm/main arm64 libopenblas-dev arm64 0.3.21+ds-4 [44.9 kB]
Get: 131 http://deb.debian.org/debian bookworm/main arm64 libopenjp2-7 arm64 2.5.0-1+b1 [176 kB]
Get: 132 http://deb.debian.org/debian bookworm/main arm64 libpgm-5.3-0 arm64 5.3.128~dfsg-2 [152 kB]
Get: 133 http://deb.debian.org/debian bookworm/main arm64 zlib1g-dev arm64 1:1.2.13.dfsg-1 [913 kB]
Get: 134 http://deb.debian.org/debian bookworm/main arm64 libpython3.11-dev arm64 3.11.2-6 [4395 kB]
Get: 135 http://deb.debian.org/debian bookworm/main arm64 libpython3-dev arm64 3.11.2-1+b1 [9564 B]
Get: 136 http://deb.debian.org/debian bookworm/main arm64 libpython3-all-dev arm64 3.11.2-1+b1 [1068 B]
Get: 137 http://deb.debian.org/debian bookworm/main arm64 libqhull-r8.0 arm64 2020.2-5 [230 kB]
Get: 138 http://deb.debian.org/debian bookworm/main arm64 libraqm0 arm64 0.7.0-4.1 [10.4 kB]
Get: 139 http://deb.debian.org/debian bookworm/main arm64 libsodium23 arm64 1.0.18-1 [119 kB]
Get: 140 http://deb.debian.org/debian bookworm/main arm64 libwebp7 arm64 1.2.4-0.1 [259 kB]
Get: 141 http://deb.debian.org/debian bookworm/main arm64 libtiff6 arm64 4.5.0-5 [300 kB]
Get: 142 http://deb.debian.org/debian bookworm/main arm64 libwebpdemux2 arm64 1.2.4-0.1 [99.1 kB]
Get: 143 http://deb.debian.org/debian bookworm/main arm64 libwebpmux3 arm64 1.2.4-0.1 [109 kB]
Get: 144 http://deb.debian.org/debian bookworm/main arm64 libxsimd-dev arm64 8.1.0-7 [88.8 kB]
Get: 145 http://deb.debian.org/debian bookworm/main arm64 libxslt1.1 arm64 1.1.35-1 [231 kB]
Get: 146 http://deb.debian.org/debian bookworm/main arm64 libzmq5 arm64 4.3.4-6 [244 kB]
Get: 147 http://deb.debian.org/debian bookworm/main arm64 python-babel-localedata all 2.10.3-1 [5615 kB]
Get: 148 http://deb.debian.org/debian bookworm/main arm64 python-matplotlib-data all 3.6.3-1 [2744 kB]
Get: 149 http://deb.debian.org/debian bookworm/main arm64 python-tables-data all 3.7.0-5 [47.2 kB]
Get: 150 http://deb.debian.org/debian bookworm/main arm64 python-tinycss2-common all 1.2.1-2 [31.5 kB]
Get: 151 http://deb.debian.org/debian bookworm/main arm64 python3-alabaster all 0.7.12-1 [20.8 kB]
Get: 152 http://deb.debian.org/debian bookworm/main arm64 python3-all arm64 3.11.2-1+b1 [1064 B]
Get: 153 http://deb.debian.org/debian bookworm/main arm64 python3.11-dev arm64 3.11.2-6 [617 kB]
Get: 154 http://deb.debian.org/debian bookworm/main arm64 python3-dev arm64 3.11.2-1+b1 [26.2 kB]
Get: 155 http://deb.debian.org/debian bookworm/main arm64 python3-all-dev arm64 3.11.2-1+b1 [1076 B]
Get: 156 http://deb.debian.org/debian bookworm/main arm64 python3-appdirs all 1.4.4-3 [13.0 kB]
Get: 157 http://deb.debian.org/debian bookworm/main arm64 python3-six all 1.16.0-4 [17.5 kB]
Get: 158 http://deb.debian.org/debian bookworm/main arm64 python3-asttokens all 2.2.1-1 [19.8 kB]
Get: 159 http://deb.debian.org/debian bookworm/main arm64 python3-astunparse all 1.6.3-2 [13.8 kB]
Get: 160 http://deb.debian.org/debian bookworm/main arm64 python3-attr all 22.2.0-1 [65.4 kB]
Get: 161 http://deb.debian.org/debian bookworm/main arm64 python3-pkg-resources all 66.1.1-1 [296 kB]
Get: 162 http://deb.debian.org/debian bookworm/main arm64 python3-tz all 2022.7.1-3 [30.1 kB]
Get: 163 http://deb.debian.org/debian bookworm/main arm64 python3-babel all 2.10.3-1 [103 kB]
Get: 164 http://deb.debian.org/debian bookworm/main arm64 python3-backcall all 0.2.0-4 [12.1 kB]
Get: 165 http://deb.debian.org/debian bookworm/main arm64 python3-gast all 0.5.2-2 [9364 B]
Get: 166 http://deb.debian.org/debian bookworm/main arm64 python3-beniget all 0.4.1-3 [9920 B]
Get: 167 http://deb.debian.org/debian bookworm/main arm64 python3-webencodings all 0.5.1-5 [11.1 kB]
Get: 168 http://deb.debian.org/debian bookworm/main arm64 python3-html5lib all 1.1-3 [93.0 kB]
Get: 169 http://deb.debian.org/debian bookworm/main arm64 python3-bleach all 5.0.1-2 [48.5 kB]
Get: 170 http://deb.debian.org/debian bookworm/main arm64 python3-brotli arm64 1.0.9-2+b6 [281 kB]
Get: 171 http://deb.debian.org/debian bookworm/main arm64 python3-soupsieve all 2.3.2-1 [38.8 kB]
Get: 172 http://deb.debian.org/debian bookworm/main arm64 python3-bs4 all 4.11.2-2 [121 kB]
Get: 173 http://deb.debian.org/debian bookworm/main arm64 python3-bytecode all 0.14.0-2 [39.9 kB]
Get: 174 http://deb.debian.org/debian bookworm/main arm64 python3-certifi all 2022.9.24-1 [153 kB]
Get: 175 http://deb.debian.org/debian bookworm/main arm64 python3-cffi-backend arm64 1.15.1-5+b1 [84.4 kB]
Get: 176 http://deb.debian.org/debian bookworm/main arm64 python3-chardet all 5.1.0+dfsg-2 [110 kB]
Get: 177 http://deb.debian.org/debian bookworm/main arm64 python3-charset-normalizer all 3.0.1-2 [49.3 kB]
Get: 178 http://deb.debian.org/debian bookworm/main arm64 python3-numpy arm64 1:1.24.2-1 [4751 kB]
Get: 179 http://deb.debian.org/debian bookworm/main arm64 python3-contourpy arm64 1.0.7-1+b1 [154 kB]
Get: 180 http://deb.debian.org/debian bookworm/main arm64 python3-coverage arm64 6.5.0+dfsg1-2+b1 [153 kB]
Get: 181 http://deb.debian.org/debian bookworm/main arm64 python3-cycler all 0.11.0-1 [8020 B]
Get: 182 http://deb.debian.org/debian bookworm/main arm64 python3-dateutil all 2.8.2-2 [78.3 kB]
Get: 183 http://deb.debian.org/debian bookworm/main arm64 python3-pydevd arm64 2.9.5+ds-4 [452 kB]
Get: 184 http://deb.debian.org/debian bookworm/main arm64 python3-debugpy all 1.6.6+ds-1 [67.7 kB]
Get: 185 http://deb.debian.org/debian bookworm/main arm64 python3-decorator all 5.1.1-3 [14.9 kB]
Get: 186 http://deb.debian.org/debian bookworm/main arm64 python3-defusedxml all 0.7.1-2 [43.3 kB]
Get: 187 http://deb.debian.org/debian bookworm/main arm64 python3-roman all 3.3-3 [9880 B]
Get: 188 http://deb.debian.org/debian bookworm/main arm64 python3-docutils all 0.19+dfsg-6 [382 kB]
Get: 189 http://deb.debian.org/debian bookworm/main arm64 python3-entrypoints all 0.4-2 [7184 B]
Get: 190 http://deb.debian.org/debian bookworm/main arm64 python3-executing all 1.2.0-2 [22.6 kB]
Get: 191 http://deb.debian.org/debian bookworm/main arm64 python3-fastjsonschema all 2.16.3-2 [21.6 kB]
Get: 192 http://deb.debian.org/debian bookworm/main arm64 python3-ply all 3.11-5 [65.8 kB]
Get: 193 http://deb.debian.org/debian bookworm/main arm64 python3-pythran arm64 0.11.0+ds-7 [427 kB]
Get: 194 http://deb.debian.org/debian bookworm/main arm64 python3-scipy arm64 1.10.1-2 [14.2 MB]
Get: 195 http://deb.debian.org/debian bookworm/main arm64 python3-ufolib2 all 0.14.0+dfsg1-1 [34.3 kB]
Get: 196 http://deb.debian.org/debian bookworm/main arm64 python3-mpmath all 1.2.1-2 [418 kB]
Get: 197 http://deb.debian.org/debian bookworm/main arm64 python3-sympy all 1.11.1-1 [4358 kB]
Get: 198 http://deb.debian.org/debian bookworm/main arm64 python3-fs all 2.4.16-2 [95.2 kB]
Get: 199 http://deb.debian.org/debian bookworm/main arm64 python3-lxml arm64 4.9.2-1+b1 [1074 kB]
Get: 200 http://deb.debian.org/debian bookworm/main arm64 python3-lz4 arm64 4.0.2+dfsg-1+b2 [25.0 kB]
Get: 201 http://deb.debian.org/debian bookworm/main arm64 unicode-data all 15.0.0-1 [7984 kB]
Get: 202 http://deb.debian.org/debian bookworm/main arm64 python3-fonttools arm64 4.38.0-1+b1 [990 kB]
Get: 203 http://deb.debian.org/debian bookworm/main arm64 python3-idna all 3.3-1 [39.4 kB]
Get: 204 http://deb.debian.org/debian bookworm/main arm64 python3-imagesize all 1.4.1-1 [6688 B]
Get: 205 http://deb.debian.org/debian bookworm/main arm64 python3-parso all 0.8.3-1 [67.4 kB]
Get: 206 http://deb.debian.org/debian bookworm/main arm64 python3-jedi all 0.18.2-1 [689 kB]
Get: 207 http://deb.debian.org/debian bookworm/main arm64 python3-traitlets all 5.5.0-1 [92.4 kB]
Get: 208 http://deb.debian.org/debian bookworm/main arm64 python3-matplotlib-inline all 0.1.6-2 [8652 B]
Get: 209 http://deb.debian.org/debian bookworm/main arm64 python3-ptyprocess all 0.7.0-5 [14.7 kB]
Get: 210 http://deb.debian.org/debian bookworm/main arm64 python3-pexpect all 4.8.0-4 [52.9 kB]
Get: 211 http://deb.debian.org/debian bookworm/main arm64 python3-pickleshare all 0.7.5-5 [7600 B]
Get: 212 http://deb.debian.org/debian bookworm/main arm64 python3-wcwidth all 0.2.5+dfsg1-1.1 [21.4 kB]
Get: 213 http://deb.debian.org/debian bookworm/main arm64 python3-prompt-toolkit all 3.0.36-2 [276 kB]
Get: 214 http://deb.debian.org/debian bookworm/main arm64 python3-pygments all 2.14.0+dfsg-1 [783 kB]
Get: 215 http://deb.debian.org/debian bookworm/main arm64 python3-pure-eval all 0.2.2-1 [11.2 kB]
Get: 216 http://deb.debian.org/debian bookworm/main arm64 python3-stack-data all 0.6.2-3 [21.8 kB]
Get: 217 http://deb.debian.org/debian bookworm/main arm64 python3-setuptools all 66.1.1-1 [521 kB]
Get: 218 http://deb.debian.org/debian bookworm/main arm64 python3-ipython all 8.5.0-4 [517 kB]
Get: 219 http://deb.debian.org/debian bookworm/main arm64 python3-jupyter-core all 4.12.0-1 [27.3 kB]
Get: 220 http://deb.debian.org/debian bookworm/main arm64 python3-nest-asyncio all 1.5.4-1 [6248 B]
Get: 221 http://deb.debian.org/debian bookworm/main arm64 python3-tornado arm64 6.2.0-3 [337 kB]
Get: 222 http://deb.debian.org/debian bookworm/main arm64 python3-py all 1.11.0-1 [89.2 kB]
Get: 223 http://deb.debian.org/debian bookworm/main arm64 python3-zmq arm64 24.0.1-4+b1 [249 kB]
Get: 224 http://deb.debian.org/debian bookworm/main arm64 python3-jupyter-client all 7.4.9-2 [103 kB]
Get: 225 http://deb.debian.org/debian bookworm/main arm64 python3-packaging all 23.0-1 [32.5 kB]
Get: 226 http://deb.debian.org/debian bookworm/main arm64 python3-psutil arm64 5.9.4-1+b1 [189 kB]
Get: 227 http://deb.debian.org/debian bookworm/main arm64 python3-ipykernel all 6.17.0-1 [109 kB]
Get: 228 http://deb.debian.org/debian bookworm/main arm64 python3-markupsafe arm64 2.1.2-1+b1 [13.3 kB]
Get: 229 http://deb.debian.org/debian bookworm/main arm64 python3-jinja2 all 3.1.2-1 [119 kB]
Get: 230 http://deb.debian.org/debian bookworm/main arm64 python3-joblib all 1.2.0-4 [211 kB]
Get: 231 http://deb.debian.org/debian bookworm/main arm64 python3-pyrsistent arm64 0.18.1-1+b3 [59.4 kB]
Get: 232 http://deb.debian.org/debian bookworm/main arm64 python3-jsonschema all 4.10.3-1 [67.9 kB]
Get: 233 http://deb.debian.org/debian bookworm/main arm64 python3-jupyterlab-pygments all 0.2.2-3 [6096 B]
Get: 234 http://deb.debian.org/debian bookworm/main arm64 python3-kiwisolver arm64 1.4.4-1+b1 [55.4 kB]
Get: 235 http://deb.debian.org/debian bookworm/main arm64 python3-pil arm64 9.4.0-1.1+b1 [452 kB]
Get: 236 http://deb.debian.org/debian bookworm/main arm64 python3-tk arm64 3.11.2-2 [97.7 kB]
Get: 237 http://deb.debian.org/debian bookworm/main arm64 python3-pil.imagetk arm64 9.4.0-1.1+b1 [74.4 kB]
Get: 238 http://deb.debian.org/debian bookworm/main arm64 python3-pyparsing all 3.0.9-1 [138 kB]
Get: 239 http://deb.debian.org/debian bookworm/main arm64 python3-matplotlib arm64 3.6.3-1+b1 [6774 kB]
Get: 240 http://deb.debian.org/debian bookworm/main arm64 sphinx-rtd-theme-common all 1.2.0+dfsg-1 [997 kB]
Get: 241 http://deb.debian.org/debian bookworm/main arm64 sphinx-common all 5.3.0-4 [653 kB]
Get: 242 http://deb.debian.org/debian bookworm/main arm64 python3-urllib3 all 1.26.12-1 [117 kB]
Get: 243 http://deb.debian.org/debian bookworm/main arm64 python3-requests all 2.28.1+dfsg-1 [67.9 kB]
Get: 244 http://deb.debian.org/debian bookworm/main arm64 python3-snowballstemmer all 2.2.0-2 [57.8 kB]
Get: 245 http://deb.debian.org/debian bookworm/main arm64 python3-sphinx all 5.3.0-4 [549 kB]
Get: 246 http://deb.debian.org/debian bookworm/main arm64 python3-sphinx-rtd-theme all 1.2.0+dfsg-1 [27.7 kB]
Get: 247 http://deb.debian.org/debian bookworm/main arm64 python3-msmb-theme all 1.2.0-3 [33.7 kB]
Get: 248 http://deb.debian.org/debian bookworm/main arm64 python3-nbformat all 5.5.0-1 [43.2 kB]
Get: 249 http://deb.debian.org/debian bookworm/main arm64 python3-nbclient all 0.7.2-1 [62.1 kB]
Get: 250 http://deb.debian.org/debian bookworm/main arm64 python3-pandocfilters all 1.5.0-1 [23.7 kB]
Get: 251 http://deb.debian.org/debian bookworm/main arm64 python3-tinycss2 all 1.2.1-2 [21.9 kB]
Get: 252 http://deb.debian.org/debian bookworm/main arm64 python3-nbconvert all 6.5.3-3 [163 kB]
Get: 253 http://deb.debian.org/debian bookworm/main arm64 python3-networkx all 2.8.8-1 [1425 kB]
Get: 254 http://deb.debian.org/debian bookworm/main arm64 python3-numexpr arm64 2.8.4-1+b2 [84.6 kB]
Get: 255 http://deb.debian.org/debian bookworm/main arm64 python3-numpydoc all 1.5.0-1 [43.0 kB]
Get: 256 http://deb.debian.org/debian bookworm/main arm64 python3-pandas-lib arm64 1.5.3+dfsg-2 [3048 kB]
Get: 257 http://deb.debian.org/debian bookworm/main arm64 python3-pandas all 1.5.3+dfsg-2 [2885 kB]
Get: 258 http://deb.debian.org/debian bookworm/main arm64 python3-threadpoolctl all 3.1.0-1 [21.2 kB]
Get: 259 http://deb.debian.org/debian bookworm/main arm64 python3-sklearn-lib arm64 1.2.1+dfsg-1 [2227 kB]
Get: 260 http://deb.debian.org/debian bookworm/main arm64 python3-sklearn all 1.2.1+dfsg-1 [2103 kB]
Get: 261 http://deb.debian.org/debian bookworm/main arm64 python3-tables-lib arm64 3.7.0-5+b1 [334 kB]
Get: 262 http://deb.debian.org/debian bookworm/main arm64 python3-tables all 3.7.0-5 [339 kB]
Fetched 161 MB in 5s (33.6 MB/s)
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Setting up cython3 (0.29.32-2+b1) ...
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Setting up python3-fastjsonschema (2.16.3-2) ...
Setting up python3-pyrsistent:arm64 (0.18.1-1+b3) ...
Setting up python3-lxml:arm64 (4.9.2-1+b1) ...
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Setting up python3-cffi-backend:arm64 (1.15.1-5+b1) ...
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Setting up python3-pkg-resources (66.1.1-1) ...
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Setting up python3-prompt-toolkit (3.0.36-2) ...
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Setting up dh-python (5.20230130) ...
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Setting up tk8.6-blt2.5 (2.5.3+dfsg-4.1) ...
Setting up python3-astunparse (1.6.3-2) ...
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Setting up libpython3-dev:arm64 (3.11.2-1+b1) ...
Setting up python3-setuptools (66.1.1-1) ...
Setting up python3-py (1.11.0-1) ...
Setting up python3-backcall (0.2.0-4) ...
Setting up python3-joblib (1.2.0-4) ...
Setting up python3-parso (0.8.3-1) ...
Setting up python3-babel (2.10.3-1) ...
update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode
Setting up python3-lz4 (4.0.2+dfsg-1+b2) ...
Setting up python3-defusedxml (0.7.1-2) ...
Setting up python3-asttokens (2.2.1-1) ...
Setting up python3.11-dev (3.11.2-6) ...
Setting up python3-charset-normalizer (3.0.1-2) ...
Setting up python3-alabaster (0.7.12-1) ...
Setting up blt (2.5.3+dfsg-4.1) ...
Setting up python3-ply (3.11-5) ...
Setting up python3-threadpoolctl (3.1.0-1) ...
Setting up python3-gast (0.5.2-2) ...
Setting up python3-all (3.11.2-1+b1) ...
Setting up python3-coverage (6.5.0+dfsg1-2+b1) ...
Setting up python3-tk:arm64 (3.11.2-2) ...
Setting up python3-networkx (2.8.8-1) ...
Setting up python3-bs4 (4.11.2-2) ...
Setting up python3-bleach (5.0.1-2) ...
Setting up python3-matplotlib-inline (0.1.6-2) ...
Setting up python3-fs (2.4.16-2) ...
Setting up python3-beniget (0.4.1-3) ...
Setting up python3-pygments (2.14.0+dfsg-1) ...
Setting up python3-chardet (5.1.0+dfsg-2) ...
Setting up python3-jsonschema (4.10.3-1) ...
Setting up python3-executing (1.2.0-2) ...
Setting up libpython3-all-dev:arm64 (3.11.2-1+b1) ...
Setting up python3-pexpect (4.8.0-4) ...
Setting up python3-zmq (24.0.1-4+b1) ...
Setting up python3-dev (3.11.2-1+b1) ...
Setting up python3-requests (2.28.1+dfsg-1) ...
Setting up python3-numpy (1:1.24.2-1) ...
Setting up python3-contourpy (1.0.7-1+b1) ...
Setting up python3-pydevd (2.9.5+ds-4) ...
Setting up python3-stack-data (0.6.2-3) ...
Setting up python3-jupyter-core (4.12.0-1) ...
Setting up python3-all-dev (3.11.2-1+b1) ...
Setting up python3-jedi (0.18.2-1) ...
Setting up python3-tables-lib (3.7.0-5+b1) ...
Setting up python3-pandas-lib:arm64 (1.5.3+dfsg-2) ...
Setting up python3-sklearn-lib:arm64 (1.2.1+dfsg-1) ...
Setting up python3-nbformat (5.5.0-1) ...
Setting up python3-debugpy (1.6.6+ds-1) ...
Setting up python3-jupyterlab-pygments (0.2.2-3) ...
Setting up python3-pandas (1.5.3+dfsg-2) ...
Setting up python3-ipython (8.5.0-4) ...
Setting up python3-numexpr (2.8.4-1+b2) ...
Setting up python3-pythran (0.11.0+ds-7) ...
Setting up python3-jupyter-client (7.4.9-2) ...
Setting up python3-scipy (1.10.1-2) ...
Setting up python3-tables (3.7.0-5) ...
Setting up python3-nbclient (0.7.2-1) ...
Setting up python3-ipykernel (6.17.0-1) ...
Setting up python3-sklearn (1.2.1+dfsg-1) ...
Setting up python3-nbconvert (6.5.3-3) ...
Setting up python3-fonttools (4.38.0-1+b1) ...
Setting up python3-pil.imagetk:arm64 (9.4.0-1.1+b1) ...
Setting up python3-ufolib2 (0.14.0+dfsg1-1) ...
Setting up python3-pil:arm64 (9.4.0-1.1+b1) ...
Setting up python3-matplotlib (3.6.3-1+b1) ...
Processing triggers for libc-bin (2.36-8) ...
Processing triggers for sgml-base (1.31) ...
Setting up docutils-common (0.19+dfsg-6) ...
Processing triggers for sgml-base (1.31) ...
Setting up python3-docutils (0.19+dfsg-6) ...
Setting up python3-sphinx (5.3.0-4) ...
Setting up python3-sphinx-rtd-theme (1.2.0+dfsg-1) ...
Setting up python3-numpydoc (1.5.0-1) ...
Setting up python3-msmb-theme (1.2.0-3) ...
Processing triggers for ca-certificates (20230311) ...
Updating certificates in /etc/ssl/certs...
0 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.
Reading package lists...
Building dependency tree...
Reading state information...
Reading extended state information...
Initializing package states...
Writing extended state information...
Building tag database...
 -> Finished parsing the build-deps
Reading package lists...
Building dependency tree...
Reading state information...
fakeroot is already the newest version (1.31-1.2).
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
I: Building the package
I: Running cd /build/mdtraj-1.9.7/ && 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_1.9.7-6_source.changes
dpkg-buildpackage: info: source package mdtraj
dpkg-buildpackage: info: source version 1.9.7-6
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Drew Parsons <dparsons@debian.org>
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture arm64
dpkg-source: info: using options from mdtraj-1.9.7/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/
 fakeroot debian/rules clean
dh clean --with python3,sphinxdoc --buildsystem=pybuild
   debian/rules override_dh_auto_clean
make[1]: Entering directory '/build/mdtraj-1.9.7'
dh_auto_clean || /bin/true
I: pybuild base:240: python3.11 setup.py clean 
Using built-in specs.
COLLECT_GCC=/usr/bin/aarch64-linux-gnu-gcc
COLLECT_LTO_WRAPPER=/usr/lib/gcc/aarch64-linux-gnu/12/lto-wrapper
Target: aarch64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Debian 12.2.0-14' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=aarch64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-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-checking=release --build=aarch64-linux-gnu --host=aarch64-linux-gnu --target=aarch64-linux-gnu
Thread model: posix
Supported LTO compression algorithms: zlib zstd
gcc version 12.2.0 (Debian 12.2.0-14) 
/build/mdtraj-1.9.7/basesetup.py:431: UserWarning: Unrecognized setuptools command ('clean'), proceeding with generating Cython sources and expanding templates
  warnings.warn("Unrecognized setuptools command ('{}'), proceeding with "
/usr/lib/python3/dist-packages/pythran/tables.py:4530: FutureWarning: In the future `np.bool` will be defined as the corresponding NumPy scalar.
  if not hasattr(numpy, method):
/usr/lib/python3/dist-packages/pythran/tables.py:4563: FutureWarning: In the future `np.bytes` will be defined as the corresponding NumPy scalar.
  obj = getattr(themodule, elem)
warning: mdtraj/formats/dcd/dcdlib.pxd:12:12: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: mdtraj/formats/dcd/dcdlib.pxd:12:16: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: mdtraj/formats/dcd/dcdlib.pxd:12:20: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
C compiler:
Attempting to autodetect OpenMP support... Compiler supports OpenMP
Attempting to autodetect SSE3   support... 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

[ 1/12] Cythonizing mdtraj/formats/binpos/binpos.pyx
[ 2/12] Cythonizing mdtraj/formats/dcd/dcd.pyx
[ 3/12] Cythonizing mdtraj/formats/dtr/dtr.pyx
[ 4/12] Cythonizing mdtraj/formats/tng/tng.pyx
[ 5/12] Cythonizing mdtraj/formats/xtc/trr.pyx
[ 6/12] Cythonizing mdtraj/formats/xtc/xtc.pyx
[ 7/12] Cythonizing mdtraj/geometry/drid.pyx
[ 8/12] Cythonizing mdtraj/geometry/neighborlist.pyx
[ 9/12] Cythonizing mdtraj/geometry/neighbors.pyx
[10/12] Cythonizing mdtraj/geometry/src/_geometry.pyx
[11/12] Cythonizing mdtraj/rmsd/_lprmsd.pyx
[12/12] Cythonizing mdtraj/rmsd/_rmsd.pyx
running clean
removing '/build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build' (and everything under it)
'build/bdist.linux-arm64' does not exist -- can't clean it
'build/scripts-3.11' does not exist -- can't clean it
for f in mdtraj/formats/binpos/binpos.c \
  mdtraj/formats/dcd/dcd.c		\
  mdtraj/formats/dtr/dtr.cpp		\
  mdtraj/formats/tng/tng.c		\
  mdtraj/formats/xtc/trr.c		\
  mdtraj/formats/xtc/xtc.c		\
  mdtraj/geometry/drid.cpp		\
  mdtraj/geometry/neighborlist.cpp	\
  mdtraj/geometry/neighbors.cpp		\
  mdtraj/geometry/src/_geometry.cpp	\
  mdtraj/rmsd/_lprmsd.cpp		\
  mdtraj/rmsd/_rmsd.cpp			\
  mdtraj/version.py;                    \
do rm -f $f; done
rm -rf __pycache__
make[1]: Leaving directory '/build/mdtraj-1.9.7'
   dh_autoreconf_clean -O--buildsystem=pybuild
   dh_clean -O--buildsystem=pybuild
 debian/rules build
dh build --with python3,sphinxdoc --buildsystem=pybuild
   dh_update_autotools_config -O--buildsystem=pybuild
   dh_autoreconf -O--buildsystem=pybuild
   dh_auto_configure -O--buildsystem=pybuild
I: pybuild base:240: python3.11 setup.py config 
Using built-in specs.
COLLECT_GCC=/usr/bin/aarch64-linux-gnu-gcc
COLLECT_LTO_WRAPPER=/usr/lib/gcc/aarch64-linux-gnu/12/lto-wrapper
Target: aarch64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Debian 12.2.0-14' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=aarch64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-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-checking=release --build=aarch64-linux-gnu --host=aarch64-linux-gnu --target=aarch64-linux-gnu
Thread model: posix
Supported LTO compression algorithms: zlib zstd
gcc version 12.2.0 (Debian 12.2.0-14) 
/build/mdtraj-1.9.7/basesetup.py:431: UserWarning: Unrecognized setuptools command ('config'), proceeding with generating Cython sources and expanding templates
  warnings.warn("Unrecognized setuptools command ('{}'), proceeding with "
/usr/lib/python3/dist-packages/pythran/tables.py:4530: FutureWarning: In the future `np.bool` will be defined as the corresponding NumPy scalar.
  if not hasattr(numpy, method):
/usr/lib/python3/dist-packages/pythran/tables.py:4563: FutureWarning: In the future `np.bytes` will be defined as the corresponding NumPy scalar.
  obj = getattr(themodule, elem)
warning: mdtraj/formats/dcd/dcdlib.pxd:12:12: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: mdtraj/formats/dcd/dcdlib.pxd:12:16: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: mdtraj/formats/dcd/dcdlib.pxd:12:20: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
C compiler:
Attempting to autodetect OpenMP support... Compiler supports OpenMP
Attempting to autodetect SSE3   support... 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

[ 1/12] Cythonizing mdtraj/formats/binpos/binpos.pyx
[ 2/12] Cythonizing mdtraj/formats/dcd/dcd.pyx
[ 3/12] Cythonizing mdtraj/formats/dtr/dtr.pyx
[ 4/12] Cythonizing mdtraj/formats/tng/tng.pyx
[ 5/12] Cythonizing mdtraj/formats/xtc/trr.pyx
[ 6/12] Cythonizing mdtraj/formats/xtc/xtc.pyx
[ 7/12] Cythonizing mdtraj/geometry/drid.pyx
[ 8/12] Cythonizing mdtraj/geometry/neighborlist.pyx
[ 9/12] Cythonizing mdtraj/geometry/neighbors.pyx
[10/12] Cythonizing mdtraj/geometry/src/_geometry.pyx
[11/12] Cythonizing mdtraj/rmsd/_lprmsd.pyx
[12/12] Cythonizing mdtraj/rmsd/_rmsd.pyx
running config
   debian/rules override_dh_auto_build-indep
make[1]: Entering directory '/build/mdtraj-1.9.7'
dh_auto_build
I: pybuild base:240: /usr/bin/python3 setup.py build 
Using built-in specs.
COLLECT_GCC=/usr/bin/aarch64-linux-gnu-gcc
COLLECT_LTO_WRAPPER=/usr/lib/gcc/aarch64-linux-gnu/12/lto-wrapper
Target: aarch64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Debian 12.2.0-14' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=aarch64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-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-checking=release --build=aarch64-linux-gnu --host=aarch64-linux-gnu --target=aarch64-linux-gnu
Thread model: posix
Supported LTO compression algorithms: zlib zstd
gcc version 12.2.0 (Debian 12.2.0-14) 
/usr/lib/python3/dist-packages/pythran/tables.py:4530: FutureWarning: In the future `np.bool` will be defined as the corresponding NumPy scalar.
  if not hasattr(numpy, method):
/usr/lib/python3/dist-packages/pythran/tables.py:4563: FutureWarning: In the future `np.bytes` will be defined as the corresponding NumPy scalar.
  obj = getattr(themodule, elem)
warning: mdtraj/formats/dcd/dcdlib.pxd:12:12: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: mdtraj/formats/dcd/dcdlib.pxd:12:16: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: mdtraj/formats/dcd/dcdlib.pxd:12:20: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
C compiler:
Attempting to autodetect OpenMP support... Compiler supports OpenMP
Attempting to autodetect SSE3   support... 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

[ 1/12] Cythonizing mdtraj/formats/binpos/binpos.pyx
[ 2/12] Cythonizing mdtraj/formats/dcd/dcd.pyx
[ 3/12] Cythonizing mdtraj/formats/dtr/dtr.pyx
[ 4/12] Cythonizing mdtraj/formats/tng/tng.pyx
[ 5/12] Cythonizing mdtraj/formats/xtc/trr.pyx
[ 6/12] Cythonizing mdtraj/formats/xtc/xtc.pyx
[ 7/12] Cythonizing mdtraj/geometry/drid.pyx
[ 8/12] Cythonizing mdtraj/geometry/neighborlist.pyx
[ 9/12] Cythonizing mdtraj/geometry/neighbors.pyx
[10/12] Cythonizing mdtraj/geometry/src/_geometry.pyx
[11/12] Cythonizing mdtraj/rmsd/_lprmsd.pyx
[12/12] Cythonizing mdtraj/rmsd/_rmsd.pyx
running build
running build_py
creating /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj
copying mdtraj/version.py -> /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj
copying mdtraj/io.py -> /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj
copying mdtraj/__init__.py -> /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj
creating /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils
copying mdtraj/utils/zipped.py -> /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils
copying mdtraj/utils/validation.py -> /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils
copying mdtraj/utils/unitcell.py -> /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils
copying mdtraj/utils/six.py -> /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils
copying mdtraj/utils/singleton.py -> /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils
copying mdtraj/utils/rotation.py -> /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils
copying mdtraj/utils/delay_import.py -> /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils
copying mdtraj/utils/contextmanagers.py -> /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils
copying mdtraj/utils/__init__.py -> /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils
creating /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/testing
copying mdtraj/testing/testing.py -> /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/testing
copying mdtraj/testing/docstrings.py -> /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/testing
copying mdtraj/testing/docscrape.py -> /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/testing
copying mdtraj/testing/__init__.py -> /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/testing
creating /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/scripts
copying mdtraj/scripts/mdinspect.py -> /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/scripts
copying mdtraj/scripts/mdconvert.py -> /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/scripts
copying mdtraj/scripts/__init__.py -> /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/scripts
creating /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/reporters
copying mdtraj/reporters/xtcreporter.py -> /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/reporters
copying mdtraj/reporters/netcdfreporter.py -> /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/reporters
copying mdtraj/reporters/hdf5reporter.py -> /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/reporters
copying mdtraj/reporters/dcdreporter.py -> /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/reporters
copying mdtraj/reporters/basereporter.py -> /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/reporters
copying mdtraj/reporters/__init__.py -> /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/reporters
creating /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/nmr
copying mdtraj/nmr/shift_wrappers.py -> /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/nmr
copying mdtraj/nmr/scalar_couplings.py -> /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/nmr
copying mdtraj/nmr/__init__.py -> /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/nmr
creating /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry
copying mdtraj/geometry/thermodynamic_properties.py -> /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry
copying mdtraj/geometry/shape.py -> /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry
copying mdtraj/geometry/sasa.py -> /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry
copying mdtraj/geometry/rg.py -> /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry
copying mdtraj/geometry/rdf.py -> /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry
copying mdtraj/geometry/order.py -> /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry
copying mdtraj/geometry/internal.py -> /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry
copying mdtraj/geometry/hbond.py -> /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry
copying mdtraj/geometry/dssp.py -> /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry
copying mdtraj/geometry/distance.py -> /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry
copying mdtraj/geometry/dihedral.py -> /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry
copying mdtraj/geometry/contact.py -> /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry
copying mdtraj/geometry/angle.py -> /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry
copying mdtraj/geometry/alignment.py -> /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry
copying mdtraj/geometry/__init__.py -> /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry
creating /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats
copying mdtraj/formats/xyzfile.py -> /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats
copying mdtraj/formats/registry.py -> /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats
copying mdtraj/formats/psf.py -> /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats
copying mdtraj/formats/prmtop.py -> /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats
copying mdtraj/formats/openmmxml.py -> /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats
copying mdtraj/formats/netcdf.py -> /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats
copying mdtraj/formats/mol2.py -> /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats
copying mdtraj/formats/mdcrd.py -> /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats
copying mdtraj/formats/lh5.py -> /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats
copying mdtraj/formats/lammpstrj.py -> /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats
copying mdtraj/formats/hoomdxml.py -> /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats
copying mdtraj/formats/hdf5.py -> /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats
copying mdtraj/formats/gsd.py -> /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats
copying mdtraj/formats/gro.py -> /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats
copying mdtraj/formats/arc.py -> /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats
copying mdtraj/formats/amberrst.py -> /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats
copying mdtraj/formats/__init__.py -> /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats
creating /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core
copying mdtraj/core/trajectory.py -> /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core
copying mdtraj/core/topology.py -> /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core
copying mdtraj/core/selection.py -> /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core
copying mdtraj/core/residue_names.py -> /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core
copying mdtraj/core/element.py -> /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core
copying mdtraj/core/__init__.py -> /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core
creating /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit
copying mdtraj/utils/unit/unit_operators.py -> /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit
copying mdtraj/utils/unit/unit_math.py -> /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit
copying mdtraj/utils/unit/unit_definitions.py -> /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit
copying mdtraj/utils/unit/standard_dimensions.py -> /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit
copying mdtraj/utils/unit/quantity.py -> /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit
copying mdtraj/utils/unit/prefix.py -> /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit
copying mdtraj/utils/unit/constants.py -> /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit
copying mdtraj/utils/unit/unit.py -> /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit
copying mdtraj/utils/unit/mymatrix.py -> /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit
copying mdtraj/utils/unit/doctests.py -> /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit
copying mdtraj/utils/unit/baseunit.py -> /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit
copying mdtraj/utils/unit/basedimension.py -> /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit
copying mdtraj/utils/unit/__init__.py -> /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit
creating /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/pdb
copying mdtraj/formats/pdb/pdbstructure.py -> /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/pdb
copying mdtraj/formats/pdb/pdbfile.py -> /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/pdb
copying mdtraj/formats/pdb/__init__.py -> /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/pdb
creating /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/pdb/data
copying mdtraj/formats/pdb/data/residues.xml -> /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/pdb/data
copying mdtraj/formats/pdb/data/pdbNames.xml -> /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/pdb/data
running build_ext
building 'mdtraj.formats.xtc' extension
INFO: C compiler: aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC

creating build
creating build/temp.linux-arm64-cpython-311
creating build/temp.linux-arm64-cpython-311/mdtraj
creating build/temp.linux-arm64-cpython-311/mdtraj/formats
creating build/temp.linux-arm64-cpython-311/mdtraj/formats/xtc
creating build/temp.linux-arm64-cpython-311/mdtraj/formats/xtc/src
INFO: compile options: '-Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c'
extra options: '-Wno-unused-function -Wno-unreachable-code -Wno-sign-compare'
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/xtc/src/xdr_seek.c
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/xtc/src/xdrfile.c
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/xtc/src/xdrfile_xtc.c
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/xtc/xtc.c
mdtraj/formats/xtc/src/xdrfile_xtc.c: In function 'xtc_coord':
mdtraj/formats/xtc/src/xdrfile_xtc.c:66:15: warning: unused variable 'j' [-Wunused-variable]
   66 |         int i,j,result;
      |               ^
mdtraj/formats/xtc/src/xdrfile_xtc.c:66:13: warning: unused variable 'i' [-Wunused-variable]
   66 |         int i,j,result;
      |             ^
mdtraj/formats/xtc/src/xdrfile_xtc.c: In function 'read_xtc_nframes':
mdtraj/formats/xtc/src/xdrfile_xtc.c:119:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  119 |     if (NULL == xd)
      |     ^~
mdtraj/formats/xtc/src/xdrfile_xtc.c:122:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  122 |         do {
      |         ^~
mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_decompress_coord_float':
mdtraj/formats/xtc/src/xdrfile.c:788:32: warning: variable 'larger' set but not used [-Wunused-but-set-variable]
  788 |         int smallnum, smaller, larger, i, is_smaller, run;
      |                                ^~~~~~
mdtraj/formats/xtc/src/xdrfile.c:785:23: warning: variable 'minidx' set but not used [-Wunused-but-set-variable]
  785 |         int smallidx, minidx, maxidx;
      |                       ^~~~~~
mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_compress_coord_float':
mdtraj/formats/xtc/src/xdrfile.c:1016:13: warning: variable 'errval' set but not used [-Wunused-but-set-variable]
 1016 |         int errval=1;
      |             ^~~~~~
mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_decompress_coord_double':
mdtraj/formats/xtc/src/xdrfile.c:1305:32: warning: variable 'larger' set but not used [-Wunused-but-set-variable]
 1305 |         int smallnum, smaller, larger, i, is_smaller, run;
      |                                ^~~~~~
mdtraj/formats/xtc/src/xdrfile.c:1302:23: warning: variable 'minidx' set but not used [-Wunused-but-set-variable]
 1302 |         int smallidx, minidx, maxidx;
      |                       ^~~~~~
mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_compress_coord_double':
mdtraj/formats/xtc/src/xdrfile.c:1509:13: warning: variable 'errval' set but not used [-Wunused-but-set-variable]
 1509 |         int errval=1;
      |             ^~~~~~
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1940,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
                 from mdtraj/formats/xtc/xtc.c:778:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   17 | #warning "Using deprecated NumPy API, disable it with " \
      |  ^~~~~~~
mdtraj/formats/xtc/xtc.c: In function '__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_16_write':
mdtraj/formats/xtc/xtc.c:690:40: warning: '__pyx_v_status' may be used uninitialized [-Wmaybe-uninitialized]
  690 |   #define PyInt_FromLong               PyLong_FromLong
      |                                        ^~~~~~~~~~~~~~~
mdtraj/formats/xtc/xtc.c:9539:7: note: '__pyx_v_status' was declared here
 9539 |   int __pyx_v_status;
      |       ^~~~~~~~~~~~~~
mdtraj/formats/xtc/xtc.c: In function '__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_12_read':
mdtraj/formats/xtc/xtc.c:8058:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized]
 8058 |             } else if (unlikely(__pyx_t_39 >= __pyx_pybuffernd_xyz_stride.diminfo[2].shape)) __pyx_t_6 = 2;
      |                       ^
mdtraj/formats/xtc/xtc.c:6461:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[2].shape' was declared here
 6461 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/xtc.c:8054:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized]
 8054 |             } else if (unlikely(__pyx_t_38 >= __pyx_pybuffernd_xyz_stride.diminfo[1].shape)) __pyx_t_6 = 1;
      |                       ^
mdtraj/formats/xtc/xtc.c:6461:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[1].shape' was declared here
 6461 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/xtc.c:8050:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized]
 8050 |             } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_xyz_stride.diminfo[0].shape)) __pyx_t_6 = 0;
      |                       ^
mdtraj/formats/xtc/xtc.c:6461:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[0].shape' was declared here
 6461 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/xtc.c:8010:23: warning: '__pyx_pybuffernd_time_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized]
 8010 |             } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_time_stride.diminfo[0].shape)) __pyx_t_6 = 0;
      |                       ^
mdtraj/formats/xtc/xtc.c:6457:21: note: '__pyx_pybuffernd_time_stride.diminfo[0].shape' was declared here
 6457 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_time_stride;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/xtc.c:7992:23: warning: '__pyx_pybuffernd_step_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized]
 7992 |             } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_step_stride.diminfo[0].shape)) __pyx_t_6 = 0;
      |                       ^
mdtraj/formats/xtc/xtc.c:6453:21: note: '__pyx_pybuffernd_step_stride.diminfo[0].shape' was declared here
 6453 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_step_stride;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/xtc.c:8068:23: warning: '__pyx_pybuffernd_prec_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized]
 8068 |             } else if (unlikely(__pyx_t_40 >= __pyx_pybuffernd_prec_stride.diminfo[0].shape)) __pyx_t_6 = 0;
      |                       ^
mdtraj/formats/xtc/xtc.c:6449:21: note: '__pyx_pybuffernd_prec_stride.diminfo[0].shape' was declared here
 6449 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_prec_stride;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/xtc.c:8030:23: warning: '__pyx_pybuffernd_box_stride.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized]
 8030 |             } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_box_stride.diminfo[2].shape)) __pyx_t_6 = 2;
      |                       ^
mdtraj/formats/xtc/xtc.c:6443:21: note: '__pyx_pybuffernd_box_stride.diminfo[2].shape' was declared here
 6443 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/xtc.c:8026:23: warning: '__pyx_pybuffernd_box_stride.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized]
 8026 |             } else if (unlikely(__pyx_t_33 >= __pyx_pybuffernd_box_stride.diminfo[1].shape)) __pyx_t_6 = 1;
      |                       ^
mdtraj/formats/xtc/xtc.c:6443:21: note: '__pyx_pybuffernd_box_stride.diminfo[1].shape' was declared here
 6443 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/xtc.c:8022:23: warning: '__pyx_pybuffernd_box_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized]
 8022 |             } else if (unlikely(__pyx_t_32 >= __pyx_pybuffernd_box_stride.diminfo[0].shape)) __pyx_t_6 = 0;
      |                       ^
mdtraj/formats/xtc/xtc.c:6443:21: note: '__pyx_pybuffernd_box_stride.diminfo[0].shape' was declared here
 6443 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/xtc.c:7645:17: warning: '__pyx_pybuffernd_framebuffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized]
 7645 |       } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_framebuffer.diminfo[1].shape)) __pyx_t_6 = 1;
      |                 ^
mdtraj/formats/xtc/xtc.c:6445:21: note: '__pyx_pybuffernd_framebuffer.diminfo[1].shape' was declared here
 6445 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_framebuffer;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/xtc.c:7641:17: warning: '__pyx_pybuffernd_framebuffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized]
 7641 |       } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_framebuffer.diminfo[0].shape)) __pyx_t_6 = 0;
      |                 ^
mdtraj/formats/xtc/xtc.c:6445:21: note: '__pyx_pybuffernd_framebuffer.diminfo[0].shape' was declared here
 6445 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_framebuffer;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
INFO: aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-cpython-311/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-arm64-cpython-311/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-arm64-cpython-311/mdtraj/formats/xtc/src/xdrfile_xtc.o build/temp.linux-arm64-cpython-311/mdtraj/formats/xtc/xtc.o -L/usr/lib/aarch64-linux-gnu -o /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/xtc.cpython-311-aarch64-linux-gnu.so
building 'mdtraj.formats.trr' extension
INFO: C compiler: aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC

INFO: compile options: '-Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c'
extra options: '-Wno-unused-function -Wno-unreachable-code -Wno-sign-compare'
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/xtc/src/xdr_seek.c
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/xtc/src/xdrfile.c
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/xtc/src/xdrfile_trr.c
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/xtc/trr.c
mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_decompress_coord_float':
mdtraj/formats/xtc/src/xdrfile.c:788:32: warning: variable 'larger' set but not used [-Wunused-but-set-variable]
  788 |         int smallnum, smaller, larger, i, is_smaller, run;
      |                                ^~~~~~
mdtraj/formats/xtc/src/xdrfile.c:785:23: warning: variable 'minidx' set but not used [-Wunused-but-set-variable]
  785 |         int smallidx, minidx, maxidx;
      |                       ^~~~~~
mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_compress_coord_float':
mdtraj/formats/xtc/src/xdrfile.c:1016:13: warning: variable 'errval' set but not used [-Wunused-but-set-variable]
 1016 |         int errval=1;
      |             ^~~~~~
mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_decompress_coord_double':
mdtraj/formats/xtc/src/xdrfile.c:1305:32: warning: variable 'larger' set but not used [-Wunused-but-set-variable]
 1305 |         int smallnum, smaller, larger, i, is_smaller, run;
      |                                ^~~~~~
mdtraj/formats/xtc/src/xdrfile.c:1302:23: warning: variable 'minidx' set but not used [-Wunused-but-set-variable]
 1302 |         int smallidx, minidx, maxidx;
      |                       ^~~~~~
mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_compress_coord_double':
mdtraj/formats/xtc/src/xdrfile.c:1509:13: warning: variable 'errval' set but not used [-Wunused-but-set-variable]
 1509 |         int errval=1;
      |             ^~~~~~
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1940,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
                 from mdtraj/formats/xtc/trr.c:778:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   17 | #warning "Using deprecated NumPy API, disable it with " \
      |  ^~~~~~~
mdtraj/formats/xtc/trr.c: In function '__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_18_write':
mdtraj/formats/xtc/trr.c:690:40: warning: '__pyx_v_status' may be used uninitialized [-Wmaybe-uninitialized]
  690 |   #define PyInt_FromLong               PyLong_FromLong
      |                                        ^~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:11065:7: note: '__pyx_v_status' was declared here
11065 |   int __pyx_v_status;
      |       ^~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c: In function '__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_14_read':
mdtraj/formats/xtc/trr.c:8418:19: warning: '__pyx_pybuffernd_forces.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized]
 8418 |         } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_forces.diminfo[2].shape)) __pyx_t_5 = 2;
      |                   ^
mdtraj/formats/xtc/trr.c:6955:21: note: '__pyx_pybuffernd_forces.diminfo[2].shape' was declared here
 6955 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_forces;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:8414:19: warning: '__pyx_pybuffernd_forces.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized]
 8414 |         } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_forces.diminfo[1].shape)) __pyx_t_5 = 1;
      |                   ^
mdtraj/formats/xtc/trr.c:6955:21: note: '__pyx_pybuffernd_forces.diminfo[1].shape' was declared here
 6955 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_forces;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:1929:90: warning: '__pyx_pybuffernd_forces.diminfo[0].strides' may be used uninitialized [-Wmaybe-uninitialized]
 1929 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2)
      |                                                                                          ^
mdtraj/formats/xtc/trr.c:6955:21: note: '__pyx_pybuffernd_forces.diminfo[0].strides' was declared here
 6955 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_forces;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:8410:19: warning: '__pyx_pybuffernd_forces.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized]
 8410 |         } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_forces.diminfo[0].shape)) __pyx_t_5 = 0;
      |                   ^
mdtraj/formats/xtc/trr.c:6955:21: note: '__pyx_pybuffernd_forces.diminfo[0].shape' was declared here
 6955 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_forces;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:8361:19: warning: '__pyx_pybuffernd_vel.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized]
 8361 |         } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_vel.diminfo[2].shape)) __pyx_t_5 = 2;
      |                   ^
mdtraj/formats/xtc/trr.c:6971:21: note: '__pyx_pybuffernd_vel.diminfo[2].shape' was declared here
 6971 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_vel;
      |                     ^~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:8357:19: warning: '__pyx_pybuffernd_vel.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized]
 8357 |         } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_vel.diminfo[1].shape)) __pyx_t_5 = 1;
      |                   ^
mdtraj/formats/xtc/trr.c:6971:21: note: '__pyx_pybuffernd_vel.diminfo[1].shape' was declared here
 6971 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_vel;
      |                     ^~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:1929:90: warning: '__pyx_pybuffernd_vel.diminfo[0].strides' may be used uninitialized [-Wmaybe-uninitialized]
 1929 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2)
      |                                                                                          ^
mdtraj/formats/xtc/trr.c:6971:21: note: '__pyx_pybuffernd_vel.diminfo[0].strides' was declared here
 6971 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_vel;
      |                     ^~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:8353:19: warning: '__pyx_pybuffernd_vel.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized]
 8353 |         } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_vel.diminfo[0].shape)) __pyx_t_5 = 0;
      |                   ^
mdtraj/formats/xtc/trr.c:6971:21: note: '__pyx_pybuffernd_vel.diminfo[0].shape' was declared here
 6971 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_vel;
      |                     ^~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:8751:17: warning: '__pyx_pybuffernd_xyz_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized]
 8751 |       } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_xyz_buffer.diminfo[1].shape)) __pyx_t_5 = 1;
      |                 ^
mdtraj/formats/xtc/trr.c:6977:21: note: '__pyx_pybuffernd_xyz_buffer.diminfo[1].shape' was declared here
 6977 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:8747:17: warning: '__pyx_pybuffernd_xyz_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized]
 8747 |       } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_xyz_buffer.diminfo[0].shape)) __pyx_t_5 = 0;
      |                 ^
mdtraj/formats/xtc/trr.c:6977:21: note: '__pyx_pybuffernd_xyz_buffer.diminfo[0].shape' was declared here
 6977 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:8592:19: warning: '__pyx_pybuffernd_vel_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized]
 8592 |         } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_vel_buffer.diminfo[1].shape)) __pyx_t_5 = 1;
      |                   ^
mdtraj/formats/xtc/trr.c:6973:21: note: '__pyx_pybuffernd_vel_buffer.diminfo[1].shape' was declared here
 6973 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:8588:19: warning: '__pyx_pybuffernd_vel_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized]
 8588 |         } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_vel_buffer.diminfo[0].shape)) __pyx_t_5 = 0;
      |                   ^
mdtraj/formats/xtc/trr.c:6973:21: note: '__pyx_pybuffernd_vel_buffer.diminfo[0].shape' was declared here
 6973 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:8644:19: warning: '__pyx_pybuffernd_forces_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized]
 8644 |         } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_forces_buffer.diminfo[1].shape)) __pyx_t_5 = 1;
      |                   ^
mdtraj/formats/xtc/trr.c:6957:21: note: '__pyx_pybuffernd_forces_buffer.diminfo[1].shape' was declared here
 6957 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_forces_buffer;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:8640:19: warning: '__pyx_pybuffernd_forces_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized]
 8640 |         } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_forces_buffer.diminfo[0].shape)) __pyx_t_5 = 0;
      |                   ^
mdtraj/formats/xtc/trr.c:6957:21: note: '__pyx_pybuffernd_forces_buffer.diminfo[0].shape' was declared here
 6957 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_forces_buffer;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
INFO: aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-cpython-311/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-arm64-cpython-311/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-arm64-cpython-311/mdtraj/formats/xtc/src/xdrfile_trr.o build/temp.linux-arm64-cpython-311/mdtraj/formats/xtc/trr.o -L/usr/lib/aarch64-linux-gnu -o /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/trr.cpython-311-aarch64-linux-gnu.so
building 'mdtraj.formats.tng' extension
INFO: C compiler: aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC

creating build/temp.linux-arm64-cpython-311/mdtraj/formats/tng
creating build/temp.linux-arm64-cpython-311/mdtraj/formats/tng/src
creating build/temp.linux-arm64-cpython-311/mdtraj/formats/tng/src/compression
creating build/temp.linux-arm64-cpython-311/mdtraj/formats/tng/src/lib
INFO: compile options: '-DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c'
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/tng/src/compression/bwlzh.c
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/tng/src/compression/bwt.c
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/tng/src/compression/coder.c
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/tng/src/compression/dict.c
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/tng/src/compression/fixpoint.c
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/tng/src/compression/huffman.c
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/tng/src/compression/huffmem.c
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/tng/src/compression/lz77.c
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/tng/src/compression/merge_sort.c
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/tng/src/compression/mtf.c
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/tng/src/compression/rle.c
mdtraj/formats/tng/src/compression/rle.c: In function 'Ptngc_comp_conv_to_rle':
mdtraj/formats/tng/src/compression/rle.c:56:16: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
   56 |           if (v==vals[i])
      |                ^~
mdtraj/formats/tng/src/compression/mtf.c: In function 'Ptngc_comp_conv_to_mtf':
mdtraj/formats/tng/src/compression/mtf.c:196:23: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
  196 |       while (dict[ptr]!=v)
      |                       ^~
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/tng/src/compression/tng_compress.c
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/tng/src/compression/vals16.c
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/tng/src/compression/warnmalloc.c
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/tng/src/compression/widemuldiv.c
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/tng/src/compression/xtc2.c
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/tng/src/compression/xtc3.c
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/tng/src/lib/md5.c
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/tng/src/lib/tng_io.c
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/tng/tng.c
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_block_header_read':
mdtraj/formats/tng/src/lib/tng_io.c:1064:57: warning: assignment to 'tng_function_status (*)(struct tng_trajectory * const,  int32_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const,  int *)'} from incompatible pointer type 'tng_function_status (*)(struct tng_trajectory * const,  uint32_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const,  unsigned int *)'} [-Wincompatible-pointer-types]
 1064 |                 tng_data->input_endianness_swap_func_32 =
      |                                                         ^
mdtraj/formats/tng/src/lib/tng_io.c:1073:57: warning: assignment to 'tng_function_status (*)(struct tng_trajectory * const,  int64_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const,  long int *)'} from incompatible pointer type 'tng_function_status (*)(struct tng_trajectory * const,  uint64_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const,  long unsigned int *)'} [-Wincompatible-pointer-types]
 1073 |                 tng_data->input_endianness_swap_func_64 =
      |                                                         ^
mdtraj/formats/tng/src/lib/tng_io.c:1089:57: warning: assignment to 'tng_function_status (*)(struct tng_trajectory * const,  int32_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const,  int *)'} from incompatible pointer type 'tng_function_status (*)(struct tng_trajectory * const,  uint32_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const,  unsigned int *)'} [-Wincompatible-pointer-types]
 1089 |                 tng_data->input_endianness_swap_func_32 =
      |                                                         ^
mdtraj/formats/tng/src/lib/tng_io.c:1098:57: warning: assignment to 'tng_function_status (*)(struct tng_trajectory * const,  int64_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const,  long int *)'} from incompatible pointer type 'tng_function_status (*)(struct tng_trajectory * const,  uint64_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const,  long unsigned int *)'} [-Wincompatible-pointer-types]
 1098 |                 tng_data->input_endianness_swap_func_64 =
      |                                                         ^
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_output_file_endianness_get':
mdtraj/formats/tng/src/lib/tng_io.c:9565:53: warning: comparison of distinct pointer types lacks a cast
 9565 |         if(tng_data->output_endianness_swap_func_32 ==
      |                                                     ^~
mdtraj/formats/tng/src/lib/tng_io.c:9570:58: warning: comparison of distinct pointer types lacks a cast
 9570 |         else if(tng_data->output_endianness_swap_func_32 ==
      |                                                          ^~
mdtraj/formats/tng/src/lib/tng_io.c:9588:53: warning: comparison of distinct pointer types lacks a cast
 9588 |         if(tng_data->output_endianness_swap_func_64 ==
      |                                                     ^~
mdtraj/formats/tng/src/lib/tng_io.c:9593:58: warning: comparison of distinct pointer types lacks a cast
 9593 |         else if(tng_data->output_endianness_swap_func_64 ==
      |                                                          ^~
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_output_file_endianness_set':
mdtraj/formats/tng/src/lib/tng_io.c:9651:54: warning: assignment to 'tng_function_status (*)(struct tng_trajectory * const,  int32_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const,  int *)'} from incompatible pointer type 'tng_function_status (*)(struct tng_trajectory * const,  uint32_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const,  unsigned int *)'} [-Wincompatible-pointer-types]
 9651 |             tng_data->output_endianness_swap_func_32 =
      |                                                      ^
mdtraj/formats/tng/src/lib/tng_io.c:9660:54: warning: assignment to 'tng_function_status (*)(struct tng_trajectory * const,  int64_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const,  long int *)'} from incompatible pointer type 'tng_function_status (*)(struct tng_trajectory * const,  uint64_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const,  long unsigned int *)'} [-Wincompatible-pointer-types]
 9660 |             tng_data->output_endianness_swap_func_64 =
      |                                                      ^
mdtraj/formats/tng/src/lib/tng_io.c:9673:54: warning: assignment to 'tng_function_status (*)(struct tng_trajectory * const,  int32_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const,  int *)'} from incompatible pointer type 'tng_function_status (*)(struct tng_trajectory * const,  uint32_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const,  unsigned int *)'} [-Wincompatible-pointer-types]
 9673 |             tng_data->output_endianness_swap_func_32 =
      |                                                      ^
mdtraj/formats/tng/src/lib/tng_io.c:9682:54: warning: assignment to 'tng_function_status (*)(struct tng_trajectory * const,  int64_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const,  long int *)'} from incompatible pointer type 'tng_function_status (*)(struct tng_trajectory * const,  uint64_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const,  long unsigned int *)'} [-Wincompatible-pointer-types]
 9682 |             tng_data->output_endianness_swap_func_64 =
      |                                                      ^
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1940,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
                 from mdtraj/formats/tng/tng.c:804:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   17 | #warning "Using deprecated NumPy API, disable it with " \
      |  ^~~~~~~
mdtraj/formats/tng/tng.c: In function '__pyx_pf_6mdtraj_7formats_3tng_17TNGTrajectoryFile___cinit__':
mdtraj/formats/tng/tng.c:3692:104: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare]
 3692 |   __pyx_t_1 = ((tng_util_trajectory_open(__pyx_v_filename, __pyx_v_self->mode, (&__pyx_v_self->_traj)) == __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
      |                                                                                                        ^~
mdtraj/formats/tng/tng.c:3747:88: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare]
 3747 |     __pyx_t_1 = ((tng_num_particles_get(__pyx_v_self->_traj, (&__pyx_v_self->n_atoms)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
      |                                                                                        ^~
mdtraj/formats/tng/tng.c:3779:90: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare]
 3779 |     __pyx_t_1 = ((tng_num_frames_get(__pyx_v_self->_traj, (&__pyx_v_self->tot_n_frames)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
      |                                                                                          ^~
mdtraj/formats/tng/tng.c:3811:95: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare]
 3811 |     __pyx_t_1 = ((tng_distance_unit_exponential_get(__pyx_v_self->_traj, (&__pyx_v_exponent)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
      |                                                                                               ^~
mdtraj/formats/tng/tng.c:3881:113: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare]
 3881 |     __pyx_t_1 = ((tng_num_frames_per_frame_set_get(__pyx_v_self->_traj, (&__pyx_v_self->_frames_per_frame_set)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
      |                                                                                                                 ^~
mdtraj/formats/tng/tng.c:3925:77: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare]
 3925 |     __pyx_t_1 = ((tng_last_program_name_set(__pyx_v_self->_traj, __pyx_t_8) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
      |                                                                             ^~
mdtraj/formats/tng/tng.c: In function '__pyx_pf_6mdtraj_7formats_3tng_17TNGTrajectoryFile_8_read_topology':
mdtraj/formats/tng/tng.c:4721:106: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare]
 4721 |     __pyx_t_7 = ((tng_chain_name_of_particle_nr_get(__pyx_v_self->_traj, __pyx_v_i, __pyx_v_text, 0x400) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
      |                                                                                                          ^~
mdtraj/formats/tng/tng.c:4766:108: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare]
 4766 |     __pyx_t_7 = ((tng_residue_name_of_particle_nr_get(__pyx_v_self->_traj, __pyx_v_i, __pyx_v_text, 0x400) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
      |                                                                                                            ^~
mdtraj/formats/tng/tng.c:4873:115: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare]
 4873 |     __pyx_t_8 = ((tng_global_residue_id_of_particle_nr_get(__pyx_v_self->_traj, __pyx_v_i, (&__pyx_v_residue_id)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
      |                                                                                                                   ^~
mdtraj/formats/tng/tng.c:4903:105: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare]
 4903 |     __pyx_t_8 = ((tng_atom_name_of_particle_nr_get(__pyx_v_self->_traj, __pyx_v_i, __pyx_v_text, 0x400) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
      |                                                                                                         ^~
mdtraj/formats/tng/tng.c:5031:105: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare]
 5031 |     __pyx_t_8 = ((tng_atom_type_of_particle_nr_get(__pyx_v_self->_traj, __pyx_v_i, __pyx_v_text, 0x400) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
      |                                                                                                         ^~
mdtraj/formats/tng/tng.c:5632:126: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare]
 5632 |   __pyx_t_7 = ((tng_molsystem_bonds_get(__pyx_v_self->_traj, (&__pyx_v_n_bonds), (&__pyx_v_from_atoms), (&__pyx_v_to_atoms)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
      |                                                                                                                              ^~
mdtraj/formats/tng/tng.c: In function '__pyx_pf_6mdtraj_7formats_3tng_17TNGTrajectoryFile_10_read_frame':
mdtraj/formats/tng/tng.c:6042:152: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare]
 6042 |     __pyx_t_1 = ((tng_util_pos_read_range(__pyx_v_self->_traj, __pyx_v_self->_pos, __pyx_v_self->_pos, (&__pyx_v_positions), (&__pyx_v_stride_length)) == __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
      |                                                                                                                                                        ^~
mdtraj/formats/tng/tng.c:6310:108: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare]
 6310 |   __pyx_t_1 = ((tng_util_time_of_frame_get(__pyx_v_self->_traj, __pyx_v_self->_pos, (&__pyx_v_frame_time)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
      |                                                                                                            ^~
mdtraj/formats/tng/tng.c:6412:304: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare]
 6412 |     __pyx_t_1 = ((tng_data_vector_interval_get(__pyx_v_self->_traj, __pyx_v_6mdtraj_7formats_3tng_TNG_TRAJ_BOX_SHAPE, __pyx_v_self->_pos, __pyx_v_self->_pos, __pyx_e_6mdtraj_7formats_3tng_TNG_USE_HASH, (&__pyx_v_box_shape), (&__pyx_v_stride_length), (&__pyx_v_n_values_per_frame), (&__pyx_v_data_type)) == __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
      |                                                                                                                                                                                                                                                                                                                ^~
mdtraj/formats/tng/tng.c: In function '__pyx_pf_6mdtraj_7formats_3tng_17TNGTrajectoryFile_16write':
mdtraj/formats/tng/tng.c:8904:94: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare]
 8904 |     __pyx_t_1 = ((tng_implicit_num_particles_set(__pyx_v_self->_traj, __pyx_v_self->n_atoms) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
      |                                                                                              ^~
mdtraj/formats/tng/tng.c:8936:75: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare]
 8936 |     __pyx_t_1 = ((tng_util_pos_write_interval_set(__pyx_v_self->_traj, 1) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
      |                                                                           ^~
mdtraj/formats/tng/tng.c:8968:81: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare]
 8968 |     __pyx_t_1 = ((tng_util_box_shape_write_interval_set(__pyx_v_self->_traj, 1) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
      |                                                                                 ^~
mdtraj/formats/tng/tng.c:9291:77: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare]
 9291 |       __pyx_t_9 = ((tng_time_per_frame_set(__pyx_v_self->_traj, __pyx_t_15) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
      |                                                                             ^~
mdtraj/formats/tng/tng.c:9482:372: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare]
 9482 |     __pyx_t_1 = ((tng_util_pos_write(__pyx_v_self->_traj, __pyx_v_self->tot_n_frames, (&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_xyz_array.rcbuffer->pybuffer.buf, __pyx_t_18, __pyx_pybuffernd_xyz_array.diminfo[0].strides, __pyx_t_19, __pyx_pybuffernd_xyz_array.diminfo[1].strides, __pyx_t_20, __pyx_pybuffernd_xyz_array.diminfo[2].strides)))) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
      |                                                                                                                                                                                                                                                                                                                                                                                    ^~
mdtraj/formats/tng/tng.c:9534:378: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare]
 9534 |     __pyx_t_1 = ((tng_util_box_shape_write(__pyx_v_self->_traj, __pyx_v_self->tot_n_frames, (&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_box_array.rcbuffer->pybuffer.buf, __pyx_t_20, __pyx_pybuffernd_box_array.diminfo[0].strides, __pyx_t_19, __pyx_pybuffernd_box_array.diminfo[1].strides, __pyx_t_18, __pyx_pybuffernd_box_array.diminfo[2].strides)))) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
      |                                                                                                                                                                                                                                                                                                                                                                                          ^~
mdtraj/formats/tng/tng.c:9596:89: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare]
 9596 |       __pyx_t_1 = ((tng_frame_set_first_frame_time_set(__pyx_v_self->_traj, __pyx_t_15) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
      |                                                                                         ^~
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_gen_data_block_add':
mdtraj/formats/tng/src/lib/tng_io.c:12613:9: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-truncation]
12613 |         strncpy(data->block_name, block_name, strlen(block_name) + 1);
      |         ^
mdtraj/formats/tng/src/lib/tng_io.c:12613:47: note: length computed here
12613 |         strncpy(data->block_name, block_name, strlen(block_name) + 1);
      |                                               ^~~~~~~~~~~~~~~~~~
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_data_block_write.isra':
mdtraj/formats/tng/src/lib/tng_io.c:5986:72: warning: 'num_first_particle' may be used uninitialized [-Wmaybe-uninitialized]
 5986 |                     for(j = num_first_particle; j < num_first_particle + n_particles;
      |                                                     ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
mdtraj/formats/tng/src/lib/tng_io.c:5684:26: note: 'num_first_particle' was declared here
 5684 |     int64_t n_particles, num_first_particle, n_frames, stride_length;
      |                          ^~~~~~~~~~~~~~~~~~
mdtraj/formats/tng/src/lib/tng_io.c:5986:72: warning: 'n_particles' may be used uninitialized [-Wmaybe-uninitialized]
 5986 |                     for(j = num_first_particle; j < num_first_particle + n_particles;
      |                                                     ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
mdtraj/formats/tng/src/lib/tng_io.c:5684:13: note: 'n_particles' was declared here
 5684 |     int64_t n_particles, num_first_particle, n_frames, stride_length;
      |             ^~~~~~~~~~~
INFO: aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-cpython-311/mdtraj/formats/tng/src/compression/bwlzh.o build/temp.linux-arm64-cpython-311/mdtraj/formats/tng/src/compression/bwt.o build/temp.linux-arm64-cpython-311/mdtraj/formats/tng/src/compression/coder.o build/temp.linux-arm64-cpython-311/mdtraj/formats/tng/src/compression/dict.o build/temp.linux-arm64-cpython-311/mdtraj/formats/tng/src/compression/fixpoint.o build/temp.linux-arm64-cpython-311/mdtraj/formats/tng/src/compression/huffman.o build/temp.linux-arm64-cpython-311/mdtraj/formats/tng/src/compression/huffmem.o build/temp.linux-arm64-cpython-311/mdtraj/formats/tng/src/compression/lz77.o build/temp.linux-arm64-cpython-311/mdtraj/formats/tng/src/compression/merge_sort.o build/temp.linux-arm64-cpython-311/mdtraj/formats/tng/src/compression/mtf.o build/temp.linux-arm64-cpython-311/mdtraj/formats/tng/src/compression/rle.o build/temp.linux-arm64-cpython-311/mdtraj/formats/tng/src/compression/tng_compress.o build/temp.linux-arm64-cpython-311/mdtraj/formats/tng/src/compression/vals16.o build/temp.linux-arm64-cpython-311/mdtraj/formats/tng/src/compression/warnmalloc.o build/temp.linux-arm64-cpython-311/mdtraj/formats/tng/src/compression/widemuldiv.o build/temp.linux-arm64-cpython-311/mdtraj/formats/tng/src/compression/xtc2.o build/temp.linux-arm64-cpython-311/mdtraj/formats/tng/src/compression/xtc3.o build/temp.linux-arm64-cpython-311/mdtraj/formats/tng/src/lib/md5.o build/temp.linux-arm64-cpython-311/mdtraj/formats/tng/src/lib/tng_io.o build/temp.linux-arm64-cpython-311/mdtraj/formats/tng/tng.o -L/usr/lib -L/usr/lib/aarch64-linux-gnu -lz -o /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/tng.cpython-311-aarch64-linux-gnu.so
building 'mdtraj.formats.dcd' extension
INFO: C compiler: aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC

creating build/temp.linux-arm64-cpython-311/mdtraj/formats/dcd
creating build/temp.linux-arm64-cpython-311/mdtraj/formats/dcd/src
INFO: compile options: '-Imdtraj/formats/dcd/include/ -Imdtraj/formats/dcd/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c'
extra options: '-Wno-unused-function -Wno-unreachable-code -Wno-sign-compare'
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/dcd/dcd.c
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/dcd/src/dcdplugin.c
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1940,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
                 from mdtraj/formats/dcd/dcd.c:776:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   17 | #warning "Using deprecated NumPy API, disable it with " \
      |  ^~~~~~~
mdtraj/formats/dcd/dcd.c: In function '__pyx_pf_6mdtraj_7formats_3dcd_17DCDTrajectoryFile_20read':
mdtraj/formats/dcd/dcd.c:688:40: warning: '__pyx_v_i' may be used uninitialized [-Wmaybe-uninitialized]
  688 |   #define PyInt_FromLong               PyLong_FromLong
      |                                        ^~~~~~~~~~~~~~~
mdtraj/formats/dcd/dcd.c:5434:7: note: '__pyx_v_i' was declared here
 5434 |   int __pyx_v_i;
      |       ^~~~~~~~~
INFO: aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-cpython-311/mdtraj/formats/dcd/dcd.o build/temp.linux-arm64-cpython-311/mdtraj/formats/dcd/src/dcdplugin.o -L/usr/lib/aarch64-linux-gnu -o /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/dcd.cpython-311-aarch64-linux-gnu.so
building 'mdtraj.formats.binpos' extension
INFO: C compiler: aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC

creating build/temp.linux-arm64-cpython-311/mdtraj/formats/binpos
creating build/temp.linux-arm64-cpython-311/mdtraj/formats/binpos/src
INFO: compile options: '-Imdtraj/formats/binpos/include/ -Imdtraj/formats/binpos/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c'
extra options: '-Wno-unused-function -Wno-unreachable-code -Wno-sign-compare'
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/binpos/binpos.c
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/binpos/src/binposplugin.c
mdtraj/formats/binpos/src/binposplugin.c: In function 'open_binpos_read':
mdtraj/formats/binpos/src/binposplugin.c:59:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
   59 |   fread(magicchar,sizeof(char),4,fd);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/binpos/src/binposplugin.c:69:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
   69 |   fread(&igarb,sizeof(int),1,fd);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1940,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
                 from mdtraj/formats/binpos/binpos.c:776:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   17 | #warning "Using deprecated NumPy API, disable it with " \
      |  ^~~~~~~
In function '__pyx_pf_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_8_read',
    inlined from '__pyx_pw_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_9_read' at mdtraj/formats/binpos/binpos.c:4980:13:
mdtraj/formats/binpos/binpos.c:5512:6: warning: '__pyx_v_status' may be used uninitialized [-Wmaybe-uninitialized]
 5512 |   if (__pyx_t_2) {
      |      ^
mdtraj/formats/binpos/binpos.c: In function '__pyx_pw_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_9_read':
mdtraj/formats/binpos/binpos.c:4992:7: note: '__pyx_v_status' was declared here
 4992 |   int __pyx_v_status;
      |       ^~~~~~~~~~~~~~
mdtraj/formats/binpos/binpos.c:688:40: warning: '__pyx_v_i' may be used uninitialized [-Wmaybe-uninitialized]
  688 |   #define PyInt_FromLong               PyLong_FromLong
      |                                        ^~~~~~~~~~~~~~~
mdtraj/formats/binpos/binpos.c:4989:7: note: '__pyx_v_i' was declared here
 4989 |   int __pyx_v_i;
      |       ^~~~~~~~~
INFO: aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-cpython-311/mdtraj/formats/binpos/binpos.o build/temp.linux-arm64-cpython-311/mdtraj/formats/binpos/src/binposplugin.o -L/usr/lib/aarch64-linux-gnu -o /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/binpos.cpython-311-aarch64-linux-gnu.so
building 'mdtraj.formats.dtr' extension
INFO: C compiler: aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC

creating build/temp.linux-arm64-cpython-311/mdtraj/formats/dtr
creating build/temp.linux-arm64-cpython-311/mdtraj/formats/dtr/src
INFO: compile options: '-DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c'
extra options: '-Wno-unused-function -Wno-unreachable-code -Wno-sign-compare'
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/dtr/dtr.cpp
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/dtr/src/dtrplugin.cxx
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1940,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
                 from mdtraj/formats/dtr/dtr.cpp:797:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   17 | #warning "Using deprecated NumPy API, disable it with " \
      |  ^~~~~~~
mdtraj/formats/dtr/src/dtrplugin.cxx: In member function 'bool desres::molfile::Timekeys::init(const std::string&)':
mdtraj/formats/dtr/src/dtrplugin.cxx: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 constructor '{anonymous}::DDException::DDException(const std::string&, int)':
mdtraj/formats/dtr/src/dtrplugin.cxx:680:43: warning: '*this.{anonymous}::DDException::eno' is used uninitialized [-Wuninitialized]
  680 |       : std::runtime_error(text + strerror(eno)), eno(_eno){}
      |                                   ~~~~~~~~^~~~~
mdtraj/formats/dtr/src/dtrplugin.cxx: In function 'void DDmkdir(const std::string&, mode_t, int, int)':
mdtraj/formats/dtr/src/dtrplugin.cxx:706:23: warning: '%03x' directive writing between 3 and 8 bytes into a region of size 6 [-Wformat-overflow=]
  706 |         sprintf(sub, "%03x/", i);
      |                       ^~~~
mdtraj/formats/dtr/src/dtrplugin.cxx:706:22: note: directive argument in the range [0, 2147483646]
  706 |         sprintf(sub, "%03x/", i);
      |                      ^~~~~~~
In file included from /usr/include/stdio.h:906,
                 from mdtraj/formats/dtr/include/molfile_plugin.h:35,
                 from mdtraj/formats/dtr/include/dtrplugin.hxx:46,
                 from mdtraj/formats/dtr/src/dtrplugin.cxx:42:
In function 'int sprintf(char*, const char*, ...)',
    inlined from 'void DDmkdir(const std::string&, mode_t, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:706:9:
/usr/include/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 ());
      |                                   ~~~~~~~~~~~~~~~~~
INFO: aarch64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-cpython-311/mdtraj/formats/dtr/dtr.o build/temp.linux-arm64-cpython-311/mdtraj/formats/dtr/src/dtrplugin.o -L/usr/lib/aarch64-linux-gnu -o /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/dtr.cpython-311-aarch64-linux-gnu.so
building 'mdtraj._rmsd' extension
INFO: C compiler: aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC

creating build/temp.linux-arm64-cpython-311/mdtraj/rmsd
creating build/temp.linux-arm64-cpython-311/mdtraj/rmsd/src
INFO: compile options: '-Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c'
extra options: '-fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare'
INFO: aarch64-linux-gnu-gcc: mdtraj/rmsd/_rmsd.cpp
INFO: aarch64-linux-gnu-gcc: mdtraj/rmsd/src/center.cpp
INFO: aarch64-linux-gnu-gcc: mdtraj/rmsd/src/rotation.cpp
INFO: aarch64-linux-gnu-gcc: mdtraj/rmsd/src/theobald_rmsd.cpp
INFO: aarch64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-cpython-311/mdtraj/rmsd/_rmsd.o build/temp.linux-arm64-cpython-311/mdtraj/rmsd/src/center.o build/temp.linux-arm64-cpython-311/mdtraj/rmsd/src/rotation.o build/temp.linux-arm64-cpython-311/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/_rmsd.cpython-311-aarch64-linux-gnu.so
building 'mdtraj._lprmsd' extension
INFO: C compiler: aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC

INFO: compile options: '-Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c'
extra options: '-fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare'
INFO: aarch64-linux-gnu-gcc: mdtraj/rmsd/_lprmsd.cpp
INFO: aarch64-linux-gnu-gcc: mdtraj/rmsd/src/Munkres.cpp
INFO: aarch64-linux-gnu-gcc: mdtraj/rmsd/src/center.cpp
INFO: aarch64-linux-gnu-gcc: mdtraj/rmsd/src/fancy_index.cpp
INFO: aarch64-linux-gnu-gcc: mdtraj/rmsd/src/rotation.cpp
INFO: aarch64-linux-gnu-gcc: mdtraj/rmsd/src/euclidean_permutation.cpp
INFO: aarch64-linux-gnu-gcc: mdtraj/rmsd/src/theobald_rmsd.cpp
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1940,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
                 from mdtraj/rmsd/_lprmsd.cpp:806:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   17 | #warning "Using deprecated NumPy API, disable it with " \
      |  ^~~~~~~
INFO: aarch64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-cpython-311/mdtraj/rmsd/_lprmsd.o build/temp.linux-arm64-cpython-311/mdtraj/rmsd/src/Munkres.o build/temp.linux-arm64-cpython-311/mdtraj/rmsd/src/center.o build/temp.linux-arm64-cpython-311/mdtraj/rmsd/src/euclidean_permutation.o build/temp.linux-arm64-cpython-311/mdtraj/rmsd/src/fancy_index.o build/temp.linux-arm64-cpython-311/mdtraj/rmsd/src/rotation.o build/temp.linux-arm64-cpython-311/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/_lprmsd.cpython-311-aarch64-linux-gnu.so
building 'mdtraj.core.lib.libtheobald' extension
INFO: C compiler: aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC

INFO: compile options: '-Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c'
extra options: '-O3 -funroll-loops --std=c++11'
INFO: aarch64-linux-gnu-gcc: mdtraj/rmsd/src/theobald_rmsd.cpp
INFO: aarch64-linux-gnu-gcc: mdtraj/rmsd/src/center.cpp
INFO: aarch64-linux-gnu-gcc-ar: adding 2 object files to /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core/lib/libtheobald.a
building 'mdtraj.geometry._geometry' extension
INFO: C compiler: aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC

creating build/temp.linux-arm64-cpython-311/mdtraj/geometry
creating build/temp.linux-arm64-cpython-311/mdtraj/geometry/src
INFO: compile options: '-Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c'
extra options: '-fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare'
INFO: aarch64-linux-gnu-gcc: mdtraj/geometry/src/_geometry.cpp
INFO: aarch64-linux-gnu-gcc: mdtraj/geometry/src/dssp.cpp
INFO: aarch64-linux-gnu-gcc: mdtraj/geometry/src/geometry.cpp
INFO: aarch64-linux-gnu-gcc: mdtraj/geometry/src/sasa.cpp
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1940,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
                 from mdtraj/geometry/src/_geometry.cpp:808:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   17 | #warning "Using deprecated NumPy API, disable it with " \
      |  ^~~~~~~
mdtraj/geometry/src/_geometry.cpp: In function 'void __pyx_f_6mdtraj_8geometry_9_geometry_make_whole(__Pyx_memviewslice, __Pyx_memviewslice, __Pyx_memviewslice)':
mdtraj/geometry/src/_geometry.cpp:6084:224: warning: '__pyx_v_delta[2]' may be used uninitialized [-Wmaybe-uninitialized]
 6084 |       (__pyx_v_offset[__pyx_v_k]) = ((*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_frame_unitcell_vectors.data + __pyx_t_8 * __pyx_v_frame_unitcell_vectors.strides[0]) )) + __pyx_t_7)) ))) * roundf(((__pyx_v_delta[2]) / (*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_frame_unitcell_vectors.data + __pyx_t_5 * __pyx_v_frame_unitcell_vectors.strides[0]) )) + __pyx_t_4)) ))))));
      |                                                                                                                                                                                                                          ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/geometry/src/_geometry.cpp:6005:9: note: '__pyx_v_delta[2]' was declared here
 6005 |   float __pyx_v_delta[3];
      |         ^~~~~~~~~~~~~
mdtraj/geometry/src/_geometry.cpp:6098:277: warning: '__pyx_v_delta[1]' may be used uninitialized [-Wmaybe-uninitialized]
 6098 |       (__pyx_v_offset[__pyx_t_9]) = ((__pyx_v_offset[__pyx_t_9]) + ((*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_frame_unitcell_vectors.data + __pyx_t_4 * __pyx_v_frame_unitcell_vectors.strides[0]) )) + __pyx_t_5)) ))) * roundf((((__pyx_v_delta[1]) - (__pyx_v_offset[1])) / (*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_frame_unitcell_vectors.data + __pyx_t_7 * __pyx_v_frame_unitcell_vectors.strides[0]) )) + __pyx_t_8)) )))))));
      |                                                                                                                                                                                                                                                                 ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
mdtraj/geometry/src/_geometry.cpp:6005:9: note: '__pyx_v_delta[1]' was declared here
 6005 |   float __pyx_v_delta[3];
      |         ^~~~~~~~~~~~~
mdtraj/geometry/src/_geometry.cpp:6098:277: warning: '__pyx_v_offset[1]' may be used uninitialized [-Wmaybe-uninitialized]
 6098 |       (__pyx_v_offset[__pyx_t_9]) = ((__pyx_v_offset[__pyx_t_9]) + ((*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_frame_unitcell_vectors.data + __pyx_t_4 * __pyx_v_frame_unitcell_vectors.strides[0]) )) + __pyx_t_5)) ))) * roundf((((__pyx_v_delta[1]) - (__pyx_v_offset[1])) / (*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_frame_unitcell_vectors.data + __pyx_t_7 * __pyx_v_frame_unitcell_vectors.strides[0]) )) + __pyx_t_8)) )))))));
      |                                                                                                                                                                                                                                                                 ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
mdtraj/geometry/src/_geometry.cpp:6004:9: note: '__pyx_v_offset[1]' was declared here
 6004 |   float __pyx_v_offset[3];
      |         ^~~~~~~~~~~~~~
INFO: aarch64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-cpython-311/mdtraj/geometry/src/_geometry.o build/temp.linux-arm64-cpython-311/mdtraj/geometry/src/dssp.o build/temp.linux-arm64-cpython-311/mdtraj/geometry/src/geometry.o build/temp.linux-arm64-cpython-311/mdtraj/geometry/src/sasa.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/_geometry.cpython-311-aarch64-linux-gnu.so
building 'mdtraj.geometry.drid' extension
INFO: C compiler: aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC

INFO: compile options: '-Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c'
extra options: '-fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare'
INFO: aarch64-linux-gnu-gcc: mdtraj/geometry/drid.cpp
INFO: aarch64-linux-gnu-gcc: mdtraj/geometry/src/dridkernels.cpp
INFO: aarch64-linux-gnu-gcc: mdtraj/geometry/src/moments.cpp
INFO: aarch64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-cpython-311/mdtraj/geometry/drid.o build/temp.linux-arm64-cpython-311/mdtraj/geometry/src/dridkernels.o build/temp.linux-arm64-cpython-311/mdtraj/geometry/src/moments.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/drid.cpython-311-aarch64-linux-gnu.so
building 'mdtraj.geometry.neighbors' extension
INFO: C compiler: aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC

INFO: compile options: '-Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c'
extra options: '-fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare'
INFO: aarch64-linux-gnu-gcc: mdtraj/geometry/neighbors.cpp
INFO: aarch64-linux-gnu-gcc: mdtraj/geometry/src/neighbors.cpp
INFO: aarch64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-cpython-311/mdtraj/geometry/neighbors.o build/temp.linux-arm64-cpython-311/mdtraj/geometry/src/neighbors.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/neighbors.cpython-311-aarch64-linux-gnu.so
building 'mdtraj.geometry.neighborlist' extension
INFO: C compiler: aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC

INFO: compile options: '-Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c'
extra options: '-fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare'
INFO: aarch64-linux-gnu-gcc: mdtraj/geometry/neighborlist.cpp
INFO: aarch64-linux-gnu-gcc: mdtraj/geometry/src/neighborlist.cpp
In constructor 'Voxels::Voxels(float, float, float, float, float, float, const float (&)[3][3], bool)',
    inlined from 'std::vector<std::vector<int> > _compute_neighborlist(const float*, int, float, const float*)' at mdtraj/geometry/src/neighborlist.cpp:377:116:
mdtraj/geometry/src/neighborlist.cpp:50:53: warning: 'periodicBoxVectors' may be used uninitialized [-Wmaybe-uninitialized]
   50 |         periodicBoxSize[0] = periodicBoxVectors[0][0];
      |                              ~~~~~~~~~~~~~~~~~~~~~~~^
mdtraj/geometry/src/neighborlist.cpp: In function 'std::vector<std::vector<int> > _compute_neighborlist(const float*, int, float, const float*)':
mdtraj/geometry/src/neighborlist.cpp:341:11: note: 'periodicBoxVectors' declared here
  341 |     float periodicBoxVectors[3][3];
      |           ^~~~~~~~~~~~~~~~~~
In constructor 'Voxels::Voxels(float, float, float, float, float, float, const float (&)[3][3], bool)',
    inlined from 'std::vector<std::vector<int> > _compute_neighborlist(const float*, int, float, const float*)' at mdtraj/geometry/src/neighborlist.cpp:377:116:
mdtraj/geometry/src/neighborlist.cpp:51:53: warning: 'periodicBoxVectors' may be used uninitialized [-Wmaybe-uninitialized]
   51 |         periodicBoxSize[1] = periodicBoxVectors[1][1];
      |                              ~~~~~~~~~~~~~~~~~~~~~~~^
mdtraj/geometry/src/neighborlist.cpp: In function 'std::vector<std::vector<int> > _compute_neighborlist(const float*, int, float, const float*)':
mdtraj/geometry/src/neighborlist.cpp:341:11: note: 'periodicBoxVectors' declared here
  341 |     float periodicBoxVectors[3][3];
      |           ^~~~~~~~~~~~~~~~~~
In constructor 'Voxels::Voxels(float, float, float, float, float, float, const float (&)[3][3], bool)',
    inlined from 'std::vector<std::vector<int> > _compute_neighborlist(const float*, int, float, const float*)' at mdtraj/geometry/src/neighborlist.cpp:377:116:
mdtraj/geometry/src/neighborlist.cpp:52:53: warning: 'periodicBoxVectors' may be used uninitialized [-Wmaybe-uninitialized]
   52 |         periodicBoxSize[2] = periodicBoxVectors[2][2];
      |                              ~~~~~~~~~~~~~~~~~~~~~~~^
mdtraj/geometry/src/neighborlist.cpp: In function 'std::vector<std::vector<int> > _compute_neighborlist(const float*, int, float, const float*)':
mdtraj/geometry/src/neighborlist.cpp:341:11: note: 'periodicBoxVectors' declared here
  341 |     float periodicBoxVectors[3][3];
      |           ^~~~~~~~~~~~~~~~~~
In constructor 'Voxels::Voxels(float, float, float, float, float, float, const float (&)[3][3], bool)',
    inlined from 'std::vector<std::vector<int> > _compute_neighborlist(const float*, int, float, const float*)' at mdtraj/geometry/src/neighborlist.cpp:377:116:
mdtraj/geometry/src/neighborlist.cpp:56:45: warning: 'periodicBoxVectors' may be used uninitialized [-Wmaybe-uninitialized]
   56 |         triclinic = (periodicBoxVectors[0][1] != 0.0 || periodicBoxVectors[0][2] != 0.0 ||
      |                      ~~~~~~~~~~~~~~~~~~~~~~~^
mdtraj/geometry/src/neighborlist.cpp: In function 'std::vector<std::vector<int> > _compute_neighborlist(const float*, int, float, const float*)':
mdtraj/geometry/src/neighborlist.cpp:341:11: note: 'periodicBoxVectors' declared here
  341 |     float periodicBoxVectors[3][3];
      |           ^~~~~~~~~~~~~~~~~~
INFO: aarch64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-cpython-311/mdtraj/geometry/neighborlist.o build/temp.linux-arm64-cpython-311/mdtraj/geometry/src/neighborlist.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/neighborlist.cpython-311-aarch64-linux-gnu.so
cp -a /build/mdtraj-1.9.7/examples /build/mdtraj-1.9.7/examples.orig
mkdir -p /build/mdtraj-1.9.7/build/html/examples/iterload
ln -s /build/mdtraj-1.9.7/examples/data /build/mdtraj-1.9.7/build/html/examples/iterload/data
sed "s|http://www.rcsb.org/pdb/files|/build/mdtraj-1.9.7/debian/external|g" -i /build/mdtraj-1.9.7/examples/*.ipynb
PYTHONPATH=/build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build \
    MPLCONFIGDIR=/build/mdtraj-1.9.7/build/matplotlib \
	make -C docs BUILDDIR=/build/mdtraj-1.9.7/build  html
make[2]: Entering directory '/build/mdtraj-1.9.7/docs'
sphinx-build -b html -d /build/mdtraj-1.9.7/build/doctrees   . /build/mdtraj-1.9.7/build/html
Running Sphinx v5.3.0
[autosummary] generating autosummary for: analysis.rst, api/reporters.rst, api/trajectory_files.rst, api/utils.rst, atom_selection.rst, building_docs.rst, examples/atom-selection.rst, examples/centroids.rst, examples/clustering.rst, examples/hbonds.rst, ..., examples/solvent-accessible-surface-area.rst, examples/two-pass-clustering.rst, faq.rst, hdf5_format.rst, index.rst, installation.rst, load_functions.rst, mdconvert.rst, new_to_python.rst, whatsnew.rst
[autosummary] generating autosummary for: /build/mdtraj-1.9.7/docs/api/generated/mdtraj.Topology.rst, /build/mdtraj-1.9.7/docs/api/generated/mdtraj.Trajectory.rst, /build/mdtraj-1.9.7/docs/api/generated/mdtraj.Trajectory.superpose.rst, /build/mdtraj-1.9.7/docs/api/generated/mdtraj.acylindricity.rst, /build/mdtraj-1.9.7/docs/api/generated/mdtraj.asphericity.rst, /build/mdtraj-1.9.7/docs/api/generated/mdtraj.baker_hubbard.rst, /build/mdtraj-1.9.7/docs/api/generated/mdtraj.chemical_shifts_ppm.rst, /build/mdtraj-1.9.7/docs/api/generated/mdtraj.chemical_shifts_shiftx2.rst, /build/mdtraj-1.9.7/docs/api/generated/mdtraj.chemical_shifts_spartaplus.rst, /build/mdtraj-1.9.7/docs/api/generated/mdtraj.compute_J3_HN_C.rst, ..., /build/mdtraj-1.9.7/docs/api/generated/mdtraj.utils.check_random_state.rst, /build/mdtraj-1.9.7/docs/api/generated/mdtraj.utils.ensure_type.rst, /build/mdtraj-1.9.7/docs/api/generated/mdtraj.utils.ilen.rst, /build/mdtraj-1.9.7/docs/api/generated/mdtraj.utils.import_.rst, /build/mdtraj-1.9.7/docs/api/generated/mdtraj.utils.in_units_of.rst, /build/mdtraj-1.9.7/docs/api/generated/mdtraj.utils.lengths_and_angles_to_box_vectors.rst, /build/mdtraj-1.9.7/docs/api/generated/mdtraj.utils.rotation_matrix_from_quaternion.rst, /build/mdtraj-1.9.7/docs/api/generated/mdtraj.utils.timing.rst, /build/mdtraj-1.9.7/docs/api/generated/mdtraj.utils.uniform_quaternion.rst, /build/mdtraj-1.9.7/docs/api/generated/mdtraj.wernet_nilsson.rst
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/usr/lib/python3/dist-packages/numpydoc/docscrape.py:460: UserWarning: potentially wrong underline length... 
Returns 
---------- in 
Get the indices of biologically-relevant groups by name.
... in the docstring of select_atom_indices in /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core/topology.py.
  warn(msg)
/usr/lib/python3/dist-packages/numpydoc/docscrape.py:460: UserWarning: potentially wrong underline length... 
Returns 
---------- in 
Get the indices of biologically-relevant groups by name.
... in the docstring of select_atom_indices in /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core/topology.py.
  warn(msg)
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/build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/shape.py:docstring of mdtraj.geometry.shape.asphericity:4: WARNING: Block quote ends without a blank line; unexpected unindent.
/build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/contact.py:docstring of mdtraj.geometry.contact.compute_contacts:4: WARNING: Block quote ends without a blank line; unexpected unindent.
/build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/contact.py:docstring of mdtraj.geometry.contact.compute_contacts:36: ERROR: Unexpected indentation.
/build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/contact.py:docstring of mdtraj.geometry.contact.compute_contacts:40: WARNING: Block quote ends without a blank line; unexpected unindent.
docstring of mdtraj.formats.dtr.load_dtr:7: ERROR: Unexpected indentation.
/build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/shape.py:docstring of mdtraj.geometry.shape.relative_shape_anisotropy:4: WARNING: Block quote ends without a blank line; unexpected unindent.
docstring of mdtraj._rmsd.rmsf:41: WARNING: Block quote ends without a blank line; unexpected unindent.
/build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/rotation.py:docstring of mdtraj.utils.rotation.uniform_quaternion:32: ERROR: Error in "rubric" directive:
no content permitted.

.. rubric:: References

 .. [R17e8d31e726c-1] K. Shoemake. Uniform random rotations. In D. Kirk, editor, Graphics
    Gems III, pages 124-132. Academic, New York, 1992.
 .. [R17e8d31e726c-2] http://planning.cs.uiuc.edu/node198.html
/build/mdtraj-1.9.7/docs/examples/atom-selection.rst:4: ERROR: Unknown directive type "notebook".

.. notebook:: examples/atom-selection.ipynb
   :skip_exceptions:
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.. notebook:: examples/centroids.ipynb
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/build/mdtraj-1.9.7/docs/examples/hbonds.rst:4: ERROR: Unknown directive type "notebook".

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/build/mdtraj-1.9.7/docs/examples/iterload.rst:4: ERROR: Unknown directive type "notebook".

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.. notebook:: examples/principal-components.ipynb
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/build/mdtraj-1.9.7/docs/examples/ramachandran-plot.rst:4: ERROR: Unknown directive type "notebook".

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   :skip_exceptions:
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   :skip_exceptions:
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   :skip_exceptions:
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/build/mdtraj-1.9.7/docs/installation.rst:1: WARNING: malformed hyperlink target.
/build/mdtraj-1.9.7/docs/mdconvert.rst:2: WARNING: Title underline too short.

``mdconvert`` (``mdconvert-mdtraj``)
=============
/build/mdtraj-1.9.7/docs/whatsnew.rst:7: WARNING: Title underline too short.

v1.9.7 (November 12, 2021)
-----------------------
looking for now-outdated files... none found
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/build/mdtraj-1.9.7/docs/faq.rst: WARNING: document isn't included in any toctree
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generating indices... genindex done
writing additional pages... search done
copying static files... done
copying extra files... done
dumping search index in English (code: en)... done
dumping object inventory... done
build succeeded, 26 warnings.

The HTML pages are in ../build/html.

Build finished. The HTML pages are in /build/mdtraj-1.9.7/build/html.
make[2]: Leaving directory '/build/mdtraj-1.9.7/docs'
for img in `find /build/mdtraj-1.9.7/build/html/examples -name *.png`; do \
    mv $img /build/mdtraj-1.9.7/build/html/examples; \
done
sed "s|/build/mdtraj-1.9.7/build/html/examples/|./|g; s|.ipynb|.ipynb.gz|g" -i /build/mdtraj-1.9.7/build/html/examples/*.html
sed "s|/build/mdtraj-1.9.7/debian/external|http://www.rcsb.org/pdb/files|g" -i /build/mdtraj-1.9.7/build/html/examples/*.html
rm /build/mdtraj-1.9.7/build/html/examples/iterload/data
rm -rf /build/mdtraj-1.9.7/examples
mv /build/mdtraj-1.9.7/examples.orig /build/mdtraj-1.9.7/examples
make[1]: Leaving directory '/build/mdtraj-1.9.7'
   dh_auto_build -O--buildsystem=pybuild -Npython-mdtraj-doc
I: pybuild base:240: /usr/bin/python3 setup.py build 
Using built-in specs.
COLLECT_GCC=/usr/bin/aarch64-linux-gnu-gcc
COLLECT_LTO_WRAPPER=/usr/lib/gcc/aarch64-linux-gnu/12/lto-wrapper
Target: aarch64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Debian 12.2.0-14' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=aarch64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-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-checking=release --build=aarch64-linux-gnu --host=aarch64-linux-gnu --target=aarch64-linux-gnu
Thread model: posix
Supported LTO compression algorithms: zlib zstd
gcc version 12.2.0 (Debian 12.2.0-14) 
/usr/lib/python3/dist-packages/pythran/tables.py:4530: FutureWarning: In the future `np.bool` will be defined as the corresponding NumPy scalar.
  if not hasattr(numpy, method):
/usr/lib/python3/dist-packages/pythran/tables.py:4563: FutureWarning: In the future `np.bytes` will be defined as the corresponding NumPy scalar.
  obj = getattr(themodule, elem)
warning: mdtraj/formats/dcd/dcdlib.pxd:12:12: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: mdtraj/formats/dcd/dcdlib.pxd:12:16: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: mdtraj/formats/dcd/dcdlib.pxd:12:20: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
C compiler:
Attempting to autodetect OpenMP support... Compiler supports OpenMP
Attempting to autodetect SSE3   support... 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

[ 1/12] Cythonizing mdtraj/formats/binpos/binpos.pyx
[ 2/12] Cythonizing mdtraj/formats/dcd/dcd.pyx
[ 3/12] Cythonizing mdtraj/formats/dtr/dtr.pyx
[ 4/12] Cythonizing mdtraj/formats/tng/tng.pyx
[ 5/12] Cythonizing mdtraj/formats/xtc/trr.pyx
[ 6/12] Cythonizing mdtraj/formats/xtc/xtc.pyx
[ 7/12] Cythonizing mdtraj/geometry/drid.pyx
[ 8/12] Cythonizing mdtraj/geometry/neighborlist.pyx
[ 9/12] Cythonizing mdtraj/geometry/neighbors.pyx
[10/12] Cythonizing mdtraj/geometry/src/_geometry.pyx
[11/12] Cythonizing mdtraj/rmsd/_lprmsd.pyx
[12/12] Cythonizing mdtraj/rmsd/_rmsd.pyx
running build
running build_py
copying mdtraj/version.py -> /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj
running build_ext
building 'mdtraj.formats.xtc' extension
INFO: C compiler: aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC

INFO: compile options: '-Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c'
extra options: '-Wno-unused-function -Wno-unreachable-code -Wno-sign-compare'
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/xtc/src/xdr_seek.c
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/xtc/src/xdrfile.c
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/xtc/src/xdrfile_xtc.c
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/xtc/xtc.c
mdtraj/formats/xtc/src/xdrfile_xtc.c: In function 'xtc_coord':
mdtraj/formats/xtc/src/xdrfile_xtc.c:66:15: warning: unused variable 'j' [-Wunused-variable]
   66 |         int i,j,result;
      |               ^
mdtraj/formats/xtc/src/xdrfile_xtc.c:66:13: warning: unused variable 'i' [-Wunused-variable]
   66 |         int i,j,result;
      |             ^
mdtraj/formats/xtc/src/xdrfile_xtc.c: In function 'read_xtc_nframes':
mdtraj/formats/xtc/src/xdrfile_xtc.c:119:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  119 |     if (NULL == xd)
      |     ^~
mdtraj/formats/xtc/src/xdrfile_xtc.c:122:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  122 |         do {
      |         ^~
mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_decompress_coord_float':
mdtraj/formats/xtc/src/xdrfile.c:788:32: warning: variable 'larger' set but not used [-Wunused-but-set-variable]
  788 |         int smallnum, smaller, larger, i, is_smaller, run;
      |                                ^~~~~~
mdtraj/formats/xtc/src/xdrfile.c:785:23: warning: variable 'minidx' set but not used [-Wunused-but-set-variable]
  785 |         int smallidx, minidx, maxidx;
      |                       ^~~~~~
mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_compress_coord_float':
mdtraj/formats/xtc/src/xdrfile.c:1016:13: warning: variable 'errval' set but not used [-Wunused-but-set-variable]
 1016 |         int errval=1;
      |             ^~~~~~
mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_decompress_coord_double':
mdtraj/formats/xtc/src/xdrfile.c:1305:32: warning: variable 'larger' set but not used [-Wunused-but-set-variable]
 1305 |         int smallnum, smaller, larger, i, is_smaller, run;
      |                                ^~~~~~
mdtraj/formats/xtc/src/xdrfile.c:1302:23: warning: variable 'minidx' set but not used [-Wunused-but-set-variable]
 1302 |         int smallidx, minidx, maxidx;
      |                       ^~~~~~
mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_compress_coord_double':
mdtraj/formats/xtc/src/xdrfile.c:1509:13: warning: variable 'errval' set but not used [-Wunused-but-set-variable]
 1509 |         int errval=1;
      |             ^~~~~~
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1940,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
                 from mdtraj/formats/xtc/xtc.c:778:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   17 | #warning "Using deprecated NumPy API, disable it with " \
      |  ^~~~~~~
mdtraj/formats/xtc/xtc.c: In function '__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_16_write':
mdtraj/formats/xtc/xtc.c:690:40: warning: '__pyx_v_status' may be used uninitialized [-Wmaybe-uninitialized]
  690 |   #define PyInt_FromLong               PyLong_FromLong
      |                                        ^~~~~~~~~~~~~~~
mdtraj/formats/xtc/xtc.c:9539:7: note: '__pyx_v_status' was declared here
 9539 |   int __pyx_v_status;
      |       ^~~~~~~~~~~~~~
mdtraj/formats/xtc/xtc.c: In function '__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_12_read':
mdtraj/formats/xtc/xtc.c:8058:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized]
 8058 |             } else if (unlikely(__pyx_t_39 >= __pyx_pybuffernd_xyz_stride.diminfo[2].shape)) __pyx_t_6 = 2;
      |                       ^
mdtraj/formats/xtc/xtc.c:6461:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[2].shape' was declared here
 6461 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/xtc.c:8054:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized]
 8054 |             } else if (unlikely(__pyx_t_38 >= __pyx_pybuffernd_xyz_stride.diminfo[1].shape)) __pyx_t_6 = 1;
      |                       ^
mdtraj/formats/xtc/xtc.c:6461:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[1].shape' was declared here
 6461 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/xtc.c:8050:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized]
 8050 |             } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_xyz_stride.diminfo[0].shape)) __pyx_t_6 = 0;
      |                       ^
mdtraj/formats/xtc/xtc.c:6461:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[0].shape' was declared here
 6461 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/xtc.c:8010:23: warning: '__pyx_pybuffernd_time_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized]
 8010 |             } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_time_stride.diminfo[0].shape)) __pyx_t_6 = 0;
      |                       ^
mdtraj/formats/xtc/xtc.c:6457:21: note: '__pyx_pybuffernd_time_stride.diminfo[0].shape' was declared here
 6457 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_time_stride;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/xtc.c:7992:23: warning: '__pyx_pybuffernd_step_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized]
 7992 |             } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_step_stride.diminfo[0].shape)) __pyx_t_6 = 0;
      |                       ^
mdtraj/formats/xtc/xtc.c:6453:21: note: '__pyx_pybuffernd_step_stride.diminfo[0].shape' was declared here
 6453 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_step_stride;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/xtc.c:8068:23: warning: '__pyx_pybuffernd_prec_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized]
 8068 |             } else if (unlikely(__pyx_t_40 >= __pyx_pybuffernd_prec_stride.diminfo[0].shape)) __pyx_t_6 = 0;
      |                       ^
mdtraj/formats/xtc/xtc.c:6449:21: note: '__pyx_pybuffernd_prec_stride.diminfo[0].shape' was declared here
 6449 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_prec_stride;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/xtc.c:8030:23: warning: '__pyx_pybuffernd_box_stride.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized]
 8030 |             } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_box_stride.diminfo[2].shape)) __pyx_t_6 = 2;
      |                       ^
mdtraj/formats/xtc/xtc.c:6443:21: note: '__pyx_pybuffernd_box_stride.diminfo[2].shape' was declared here
 6443 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/xtc.c:8026:23: warning: '__pyx_pybuffernd_box_stride.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized]
 8026 |             } else if (unlikely(__pyx_t_33 >= __pyx_pybuffernd_box_stride.diminfo[1].shape)) __pyx_t_6 = 1;
      |                       ^
mdtraj/formats/xtc/xtc.c:6443:21: note: '__pyx_pybuffernd_box_stride.diminfo[1].shape' was declared here
 6443 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/xtc.c:8022:23: warning: '__pyx_pybuffernd_box_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized]
 8022 |             } else if (unlikely(__pyx_t_32 >= __pyx_pybuffernd_box_stride.diminfo[0].shape)) __pyx_t_6 = 0;
      |                       ^
mdtraj/formats/xtc/xtc.c:6443:21: note: '__pyx_pybuffernd_box_stride.diminfo[0].shape' was declared here
 6443 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/xtc.c:7645:17: warning: '__pyx_pybuffernd_framebuffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized]
 7645 |       } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_framebuffer.diminfo[1].shape)) __pyx_t_6 = 1;
      |                 ^
mdtraj/formats/xtc/xtc.c:6445:21: note: '__pyx_pybuffernd_framebuffer.diminfo[1].shape' was declared here
 6445 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_framebuffer;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/xtc.c:7641:17: warning: '__pyx_pybuffernd_framebuffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized]
 7641 |       } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_framebuffer.diminfo[0].shape)) __pyx_t_6 = 0;
      |                 ^
mdtraj/formats/xtc/xtc.c:6445:21: note: '__pyx_pybuffernd_framebuffer.diminfo[0].shape' was declared here
 6445 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_framebuffer;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
INFO: aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-cpython-311/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-arm64-cpython-311/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-arm64-cpython-311/mdtraj/formats/xtc/src/xdrfile_xtc.o build/temp.linux-arm64-cpython-311/mdtraj/formats/xtc/xtc.o -L/usr/lib/aarch64-linux-gnu -o /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/xtc.cpython-311-aarch64-linux-gnu.so
building 'mdtraj.formats.trr' extension
INFO: C compiler: aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC

INFO: compile options: '-Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c'
extra options: '-Wno-unused-function -Wno-unreachable-code -Wno-sign-compare'
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/xtc/src/xdr_seek.c
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/xtc/src/xdrfile.c
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/xtc/src/xdrfile_trr.c
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/xtc/trr.c
mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_decompress_coord_float':
mdtraj/formats/xtc/src/xdrfile.c:788:32: warning: variable 'larger' set but not used [-Wunused-but-set-variable]
  788 |         int smallnum, smaller, larger, i, is_smaller, run;
      |                                ^~~~~~
mdtraj/formats/xtc/src/xdrfile.c:785:23: warning: variable 'minidx' set but not used [-Wunused-but-set-variable]
  785 |         int smallidx, minidx, maxidx;
      |                       ^~~~~~
mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_compress_coord_float':
mdtraj/formats/xtc/src/xdrfile.c:1016:13: warning: variable 'errval' set but not used [-Wunused-but-set-variable]
 1016 |         int errval=1;
      |             ^~~~~~
mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_decompress_coord_double':
mdtraj/formats/xtc/src/xdrfile.c:1305:32: warning: variable 'larger' set but not used [-Wunused-but-set-variable]
 1305 |         int smallnum, smaller, larger, i, is_smaller, run;
      |                                ^~~~~~
mdtraj/formats/xtc/src/xdrfile.c:1302:23: warning: variable 'minidx' set but not used [-Wunused-but-set-variable]
 1302 |         int smallidx, minidx, maxidx;
      |                       ^~~~~~
mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_compress_coord_double':
mdtraj/formats/xtc/src/xdrfile.c:1509:13: warning: variable 'errval' set but not used [-Wunused-but-set-variable]
 1509 |         int errval=1;
      |             ^~~~~~
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1940,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
                 from mdtraj/formats/xtc/trr.c:778:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   17 | #warning "Using deprecated NumPy API, disable it with " \
      |  ^~~~~~~
mdtraj/formats/xtc/trr.c: In function '__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_18_write':
mdtraj/formats/xtc/trr.c:690:40: warning: '__pyx_v_status' may be used uninitialized [-Wmaybe-uninitialized]
  690 |   #define PyInt_FromLong               PyLong_FromLong
      |                                        ^~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:11065:7: note: '__pyx_v_status' was declared here
11065 |   int __pyx_v_status;
      |       ^~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c: In function '__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_14_read':
mdtraj/formats/xtc/trr.c:8418:19: warning: '__pyx_pybuffernd_forces.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized]
 8418 |         } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_forces.diminfo[2].shape)) __pyx_t_5 = 2;
      |                   ^
mdtraj/formats/xtc/trr.c:6955:21: note: '__pyx_pybuffernd_forces.diminfo[2].shape' was declared here
 6955 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_forces;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:8414:19: warning: '__pyx_pybuffernd_forces.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized]
 8414 |         } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_forces.diminfo[1].shape)) __pyx_t_5 = 1;
      |                   ^
mdtraj/formats/xtc/trr.c:6955:21: note: '__pyx_pybuffernd_forces.diminfo[1].shape' was declared here
 6955 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_forces;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:1929:90: warning: '__pyx_pybuffernd_forces.diminfo[0].strides' may be used uninitialized [-Wmaybe-uninitialized]
 1929 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2)
      |                                                                                          ^
mdtraj/formats/xtc/trr.c:6955:21: note: '__pyx_pybuffernd_forces.diminfo[0].strides' was declared here
 6955 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_forces;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:8410:19: warning: '__pyx_pybuffernd_forces.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized]
 8410 |         } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_forces.diminfo[0].shape)) __pyx_t_5 = 0;
      |                   ^
mdtraj/formats/xtc/trr.c:6955:21: note: '__pyx_pybuffernd_forces.diminfo[0].shape' was declared here
 6955 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_forces;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:8361:19: warning: '__pyx_pybuffernd_vel.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized]
 8361 |         } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_vel.diminfo[2].shape)) __pyx_t_5 = 2;
      |                   ^
mdtraj/formats/xtc/trr.c:6971:21: note: '__pyx_pybuffernd_vel.diminfo[2].shape' was declared here
 6971 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_vel;
      |                     ^~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:8357:19: warning: '__pyx_pybuffernd_vel.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized]
 8357 |         } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_vel.diminfo[1].shape)) __pyx_t_5 = 1;
      |                   ^
mdtraj/formats/xtc/trr.c:6971:21: note: '__pyx_pybuffernd_vel.diminfo[1].shape' was declared here
 6971 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_vel;
      |                     ^~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:1929:90: warning: '__pyx_pybuffernd_vel.diminfo[0].strides' may be used uninitialized [-Wmaybe-uninitialized]
 1929 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2)
      |                                                                                          ^
mdtraj/formats/xtc/trr.c:6971:21: note: '__pyx_pybuffernd_vel.diminfo[0].strides' was declared here
 6971 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_vel;
      |                     ^~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:8353:19: warning: '__pyx_pybuffernd_vel.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized]
 8353 |         } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_vel.diminfo[0].shape)) __pyx_t_5 = 0;
      |                   ^
mdtraj/formats/xtc/trr.c:6971:21: note: '__pyx_pybuffernd_vel.diminfo[0].shape' was declared here
 6971 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_vel;
      |                     ^~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:8751:17: warning: '__pyx_pybuffernd_xyz_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized]
 8751 |       } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_xyz_buffer.diminfo[1].shape)) __pyx_t_5 = 1;
      |                 ^
mdtraj/formats/xtc/trr.c:6977:21: note: '__pyx_pybuffernd_xyz_buffer.diminfo[1].shape' was declared here
 6977 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:8747:17: warning: '__pyx_pybuffernd_xyz_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized]
 8747 |       } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_xyz_buffer.diminfo[0].shape)) __pyx_t_5 = 0;
      |                 ^
mdtraj/formats/xtc/trr.c:6977:21: note: '__pyx_pybuffernd_xyz_buffer.diminfo[0].shape' was declared here
 6977 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:8592:19: warning: '__pyx_pybuffernd_vel_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized]
 8592 |         } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_vel_buffer.diminfo[1].shape)) __pyx_t_5 = 1;
      |                   ^
mdtraj/formats/xtc/trr.c:6973:21: note: '__pyx_pybuffernd_vel_buffer.diminfo[1].shape' was declared here
 6973 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:8588:19: warning: '__pyx_pybuffernd_vel_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized]
 8588 |         } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_vel_buffer.diminfo[0].shape)) __pyx_t_5 = 0;
      |                   ^
mdtraj/formats/xtc/trr.c:6973:21: note: '__pyx_pybuffernd_vel_buffer.diminfo[0].shape' was declared here
 6973 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:8644:19: warning: '__pyx_pybuffernd_forces_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized]
 8644 |         } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_forces_buffer.diminfo[1].shape)) __pyx_t_5 = 1;
      |                   ^
mdtraj/formats/xtc/trr.c:6957:21: note: '__pyx_pybuffernd_forces_buffer.diminfo[1].shape' was declared here
 6957 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_forces_buffer;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:8640:19: warning: '__pyx_pybuffernd_forces_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized]
 8640 |         } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_forces_buffer.diminfo[0].shape)) __pyx_t_5 = 0;
      |                   ^
mdtraj/formats/xtc/trr.c:6957:21: note: '__pyx_pybuffernd_forces_buffer.diminfo[0].shape' was declared here
 6957 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_forces_buffer;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
INFO: aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-cpython-311/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-arm64-cpython-311/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-arm64-cpython-311/mdtraj/formats/xtc/src/xdrfile_trr.o build/temp.linux-arm64-cpython-311/mdtraj/formats/xtc/trr.o -L/usr/lib/aarch64-linux-gnu -o /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/trr.cpython-311-aarch64-linux-gnu.so
building 'mdtraj.formats.tng' extension
INFO: C compiler: aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC

INFO: compile options: '-DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c'
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/tng/src/compression/bwlzh.c
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/tng/src/compression/bwt.c
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/tng/src/compression/coder.c
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/tng/src/compression/dict.c
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/tng/src/compression/fixpoint.c
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/tng/src/compression/huffman.c
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/tng/src/compression/huffmem.c
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/tng/src/compression/lz77.c
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/tng/src/compression/merge_sort.c
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/tng/src/compression/mtf.c
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/tng/src/compression/rle.c
mdtraj/formats/tng/src/compression/mtf.c: In function 'Ptngc_comp_conv_to_mtf':
mdtraj/formats/tng/src/compression/mtf.c:196:23: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
  196 |       while (dict[ptr]!=v)
      |                       ^~
mdtraj/formats/tng/src/compression/rle.c: In function 'Ptngc_comp_conv_to_rle':
mdtraj/formats/tng/src/compression/rle.c:56:16: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
   56 |           if (v==vals[i])
      |                ^~
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/tng/src/compression/tng_compress.c
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/tng/src/compression/vals16.c
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/tng/src/compression/warnmalloc.c
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/tng/src/compression/widemuldiv.c
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/tng/src/compression/xtc2.c
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/tng/src/compression/xtc3.c
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/tng/src/lib/md5.c
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/tng/src/lib/tng_io.c
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/tng/tng.c
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_block_header_read':
mdtraj/formats/tng/src/lib/tng_io.c:1064:57: warning: assignment to 'tng_function_status (*)(struct tng_trajectory * const,  int32_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const,  int *)'} from incompatible pointer type 'tng_function_status (*)(struct tng_trajectory * const,  uint32_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const,  unsigned int *)'} [-Wincompatible-pointer-types]
 1064 |                 tng_data->input_endianness_swap_func_32 =
      |                                                         ^
mdtraj/formats/tng/src/lib/tng_io.c:1073:57: warning: assignment to 'tng_function_status (*)(struct tng_trajectory * const,  int64_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const,  long int *)'} from incompatible pointer type 'tng_function_status (*)(struct tng_trajectory * const,  uint64_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const,  long unsigned int *)'} [-Wincompatible-pointer-types]
 1073 |                 tng_data->input_endianness_swap_func_64 =
      |                                                         ^
mdtraj/formats/tng/src/lib/tng_io.c:1089:57: warning: assignment to 'tng_function_status (*)(struct tng_trajectory * const,  int32_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const,  int *)'} from incompatible pointer type 'tng_function_status (*)(struct tng_trajectory * const,  uint32_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const,  unsigned int *)'} [-Wincompatible-pointer-types]
 1089 |                 tng_data->input_endianness_swap_func_32 =
      |                                                         ^
mdtraj/formats/tng/src/lib/tng_io.c:1098:57: warning: assignment to 'tng_function_status (*)(struct tng_trajectory * const,  int64_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const,  long int *)'} from incompatible pointer type 'tng_function_status (*)(struct tng_trajectory * const,  uint64_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const,  long unsigned int *)'} [-Wincompatible-pointer-types]
 1098 |                 tng_data->input_endianness_swap_func_64 =
      |                                                         ^
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_output_file_endianness_get':
mdtraj/formats/tng/src/lib/tng_io.c:9565:53: warning: comparison of distinct pointer types lacks a cast
 9565 |         if(tng_data->output_endianness_swap_func_32 ==
      |                                                     ^~
mdtraj/formats/tng/src/lib/tng_io.c:9570:58: warning: comparison of distinct pointer types lacks a cast
 9570 |         else if(tng_data->output_endianness_swap_func_32 ==
      |                                                          ^~
mdtraj/formats/tng/src/lib/tng_io.c:9588:53: warning: comparison of distinct pointer types lacks a cast
 9588 |         if(tng_data->output_endianness_swap_func_64 ==
      |                                                     ^~
mdtraj/formats/tng/src/lib/tng_io.c:9593:58: warning: comparison of distinct pointer types lacks a cast
 9593 |         else if(tng_data->output_endianness_swap_func_64 ==
      |                                                          ^~
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_output_file_endianness_set':
mdtraj/formats/tng/src/lib/tng_io.c:9651:54: warning: assignment to 'tng_function_status (*)(struct tng_trajectory * const,  int32_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const,  int *)'} from incompatible pointer type 'tng_function_status (*)(struct tng_trajectory * const,  uint32_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const,  unsigned int *)'} [-Wincompatible-pointer-types]
 9651 |             tng_data->output_endianness_swap_func_32 =
      |                                                      ^
mdtraj/formats/tng/src/lib/tng_io.c:9660:54: warning: assignment to 'tng_function_status (*)(struct tng_trajectory * const,  int64_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const,  long int *)'} from incompatible pointer type 'tng_function_status (*)(struct tng_trajectory * const,  uint64_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const,  long unsigned int *)'} [-Wincompatible-pointer-types]
 9660 |             tng_data->output_endianness_swap_func_64 =
      |                                                      ^
mdtraj/formats/tng/src/lib/tng_io.c:9673:54: warning: assignment to 'tng_function_status (*)(struct tng_trajectory * const,  int32_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const,  int *)'} from incompatible pointer type 'tng_function_status (*)(struct tng_trajectory * const,  uint32_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const,  unsigned int *)'} [-Wincompatible-pointer-types]
 9673 |             tng_data->output_endianness_swap_func_32 =
      |                                                      ^
mdtraj/formats/tng/src/lib/tng_io.c:9682:54: warning: assignment to 'tng_function_status (*)(struct tng_trajectory * const,  int64_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const,  long int *)'} from incompatible pointer type 'tng_function_status (*)(struct tng_trajectory * const,  uint64_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const,  long unsigned int *)'} [-Wincompatible-pointer-types]
 9682 |             tng_data->output_endianness_swap_func_64 =
      |                                                      ^
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1940,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
                 from mdtraj/formats/tng/tng.c:804:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   17 | #warning "Using deprecated NumPy API, disable it with " \
      |  ^~~~~~~
mdtraj/formats/tng/tng.c: In function '__pyx_pf_6mdtraj_7formats_3tng_17TNGTrajectoryFile___cinit__':
mdtraj/formats/tng/tng.c:3692:104: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare]
 3692 |   __pyx_t_1 = ((tng_util_trajectory_open(__pyx_v_filename, __pyx_v_self->mode, (&__pyx_v_self->_traj)) == __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
      |                                                                                                        ^~
mdtraj/formats/tng/tng.c:3747:88: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare]
 3747 |     __pyx_t_1 = ((tng_num_particles_get(__pyx_v_self->_traj, (&__pyx_v_self->n_atoms)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
      |                                                                                        ^~
mdtraj/formats/tng/tng.c:3779:90: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare]
 3779 |     __pyx_t_1 = ((tng_num_frames_get(__pyx_v_self->_traj, (&__pyx_v_self->tot_n_frames)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
      |                                                                                          ^~
mdtraj/formats/tng/tng.c:3811:95: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare]
 3811 |     __pyx_t_1 = ((tng_distance_unit_exponential_get(__pyx_v_self->_traj, (&__pyx_v_exponent)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
      |                                                                                               ^~
mdtraj/formats/tng/tng.c:3881:113: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare]
 3881 |     __pyx_t_1 = ((tng_num_frames_per_frame_set_get(__pyx_v_self->_traj, (&__pyx_v_self->_frames_per_frame_set)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
      |                                                                                                                 ^~
mdtraj/formats/tng/tng.c:3925:77: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare]
 3925 |     __pyx_t_1 = ((tng_last_program_name_set(__pyx_v_self->_traj, __pyx_t_8) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
      |                                                                             ^~
mdtraj/formats/tng/tng.c: In function '__pyx_pf_6mdtraj_7formats_3tng_17TNGTrajectoryFile_8_read_topology':
mdtraj/formats/tng/tng.c:4721:106: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare]
 4721 |     __pyx_t_7 = ((tng_chain_name_of_particle_nr_get(__pyx_v_self->_traj, __pyx_v_i, __pyx_v_text, 0x400) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
      |                                                                                                          ^~
mdtraj/formats/tng/tng.c:4766:108: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare]
 4766 |     __pyx_t_7 = ((tng_residue_name_of_particle_nr_get(__pyx_v_self->_traj, __pyx_v_i, __pyx_v_text, 0x400) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
      |                                                                                                            ^~
mdtraj/formats/tng/tng.c:4873:115: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare]
 4873 |     __pyx_t_8 = ((tng_global_residue_id_of_particle_nr_get(__pyx_v_self->_traj, __pyx_v_i, (&__pyx_v_residue_id)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
      |                                                                                                                   ^~
mdtraj/formats/tng/tng.c:4903:105: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare]
 4903 |     __pyx_t_8 = ((tng_atom_name_of_particle_nr_get(__pyx_v_self->_traj, __pyx_v_i, __pyx_v_text, 0x400) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
      |                                                                                                         ^~
mdtraj/formats/tng/tng.c:5031:105: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare]
 5031 |     __pyx_t_8 = ((tng_atom_type_of_particle_nr_get(__pyx_v_self->_traj, __pyx_v_i, __pyx_v_text, 0x400) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
      |                                                                                                         ^~
mdtraj/formats/tng/tng.c:5632:126: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare]
 5632 |   __pyx_t_7 = ((tng_molsystem_bonds_get(__pyx_v_self->_traj, (&__pyx_v_n_bonds), (&__pyx_v_from_atoms), (&__pyx_v_to_atoms)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
      |                                                                                                                              ^~
mdtraj/formats/tng/tng.c: In function '__pyx_pf_6mdtraj_7formats_3tng_17TNGTrajectoryFile_10_read_frame':
mdtraj/formats/tng/tng.c:6042:152: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare]
 6042 |     __pyx_t_1 = ((tng_util_pos_read_range(__pyx_v_self->_traj, __pyx_v_self->_pos, __pyx_v_self->_pos, (&__pyx_v_positions), (&__pyx_v_stride_length)) == __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
      |                                                                                                                                                        ^~
mdtraj/formats/tng/tng.c:6310:108: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare]
 6310 |   __pyx_t_1 = ((tng_util_time_of_frame_get(__pyx_v_self->_traj, __pyx_v_self->_pos, (&__pyx_v_frame_time)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
      |                                                                                                            ^~
mdtraj/formats/tng/tng.c:6412:304: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare]
 6412 |     __pyx_t_1 = ((tng_data_vector_interval_get(__pyx_v_self->_traj, __pyx_v_6mdtraj_7formats_3tng_TNG_TRAJ_BOX_SHAPE, __pyx_v_self->_pos, __pyx_v_self->_pos, __pyx_e_6mdtraj_7formats_3tng_TNG_USE_HASH, (&__pyx_v_box_shape), (&__pyx_v_stride_length), (&__pyx_v_n_values_per_frame), (&__pyx_v_data_type)) == __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
      |                                                                                                                                                                                                                                                                                                                ^~
mdtraj/formats/tng/tng.c: In function '__pyx_pf_6mdtraj_7formats_3tng_17TNGTrajectoryFile_16write':
mdtraj/formats/tng/tng.c:8904:94: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare]
 8904 |     __pyx_t_1 = ((tng_implicit_num_particles_set(__pyx_v_self->_traj, __pyx_v_self->n_atoms) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
      |                                                                                              ^~
mdtraj/formats/tng/tng.c:8936:75: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare]
 8936 |     __pyx_t_1 = ((tng_util_pos_write_interval_set(__pyx_v_self->_traj, 1) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
      |                                                                           ^~
mdtraj/formats/tng/tng.c:8968:81: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare]
 8968 |     __pyx_t_1 = ((tng_util_box_shape_write_interval_set(__pyx_v_self->_traj, 1) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
      |                                                                                 ^~
mdtraj/formats/tng/tng.c:9291:77: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare]
 9291 |       __pyx_t_9 = ((tng_time_per_frame_set(__pyx_v_self->_traj, __pyx_t_15) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
      |                                                                             ^~
mdtraj/formats/tng/tng.c:9482:372: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare]
 9482 |     __pyx_t_1 = ((tng_util_pos_write(__pyx_v_self->_traj, __pyx_v_self->tot_n_frames, (&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_xyz_array.rcbuffer->pybuffer.buf, __pyx_t_18, __pyx_pybuffernd_xyz_array.diminfo[0].strides, __pyx_t_19, __pyx_pybuffernd_xyz_array.diminfo[1].strides, __pyx_t_20, __pyx_pybuffernd_xyz_array.diminfo[2].strides)))) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
      |                                                                                                                                                                                                                                                                                                                                                                                    ^~
mdtraj/formats/tng/tng.c:9534:378: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare]
 9534 |     __pyx_t_1 = ((tng_util_box_shape_write(__pyx_v_self->_traj, __pyx_v_self->tot_n_frames, (&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_box_array.rcbuffer->pybuffer.buf, __pyx_t_20, __pyx_pybuffernd_box_array.diminfo[0].strides, __pyx_t_19, __pyx_pybuffernd_box_array.diminfo[1].strides, __pyx_t_18, __pyx_pybuffernd_box_array.diminfo[2].strides)))) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
      |                                                                                                                                                                                                                                                                                                                                                                                          ^~
mdtraj/formats/tng/tng.c:9596:89: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare]
 9596 |       __pyx_t_1 = ((tng_frame_set_first_frame_time_set(__pyx_v_self->_traj, __pyx_t_15) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
      |                                                                                         ^~
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_gen_data_block_add':
mdtraj/formats/tng/src/lib/tng_io.c:12613:9: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-truncation]
12613 |         strncpy(data->block_name, block_name, strlen(block_name) + 1);
      |         ^
mdtraj/formats/tng/src/lib/tng_io.c:12613:47: note: length computed here
12613 |         strncpy(data->block_name, block_name, strlen(block_name) + 1);
      |                                               ^~~~~~~~~~~~~~~~~~
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_data_block_write.isra':
mdtraj/formats/tng/src/lib/tng_io.c:5986:72: warning: 'num_first_particle' may be used uninitialized [-Wmaybe-uninitialized]
 5986 |                     for(j = num_first_particle; j < num_first_particle + n_particles;
      |                                                     ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
mdtraj/formats/tng/src/lib/tng_io.c:5684:26: note: 'num_first_particle' was declared here
 5684 |     int64_t n_particles, num_first_particle, n_frames, stride_length;
      |                          ^~~~~~~~~~~~~~~~~~
mdtraj/formats/tng/src/lib/tng_io.c:5986:72: warning: 'n_particles' may be used uninitialized [-Wmaybe-uninitialized]
 5986 |                     for(j = num_first_particle; j < num_first_particle + n_particles;
      |                                                     ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
mdtraj/formats/tng/src/lib/tng_io.c:5684:13: note: 'n_particles' was declared here
 5684 |     int64_t n_particles, num_first_particle, n_frames, stride_length;
      |             ^~~~~~~~~~~
INFO: aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-cpython-311/mdtraj/formats/tng/src/compression/bwlzh.o build/temp.linux-arm64-cpython-311/mdtraj/formats/tng/src/compression/bwt.o build/temp.linux-arm64-cpython-311/mdtraj/formats/tng/src/compression/coder.o build/temp.linux-arm64-cpython-311/mdtraj/formats/tng/src/compression/dict.o build/temp.linux-arm64-cpython-311/mdtraj/formats/tng/src/compression/fixpoint.o build/temp.linux-arm64-cpython-311/mdtraj/formats/tng/src/compression/huffman.o build/temp.linux-arm64-cpython-311/mdtraj/formats/tng/src/compression/huffmem.o build/temp.linux-arm64-cpython-311/mdtraj/formats/tng/src/compression/lz77.o build/temp.linux-arm64-cpython-311/mdtraj/formats/tng/src/compression/merge_sort.o build/temp.linux-arm64-cpython-311/mdtraj/formats/tng/src/compression/mtf.o build/temp.linux-arm64-cpython-311/mdtraj/formats/tng/src/compression/rle.o build/temp.linux-arm64-cpython-311/mdtraj/formats/tng/src/compression/tng_compress.o build/temp.linux-arm64-cpython-311/mdtraj/formats/tng/src/compression/vals16.o build/temp.linux-arm64-cpython-311/mdtraj/formats/tng/src/compression/warnmalloc.o build/temp.linux-arm64-cpython-311/mdtraj/formats/tng/src/compression/widemuldiv.o build/temp.linux-arm64-cpython-311/mdtraj/formats/tng/src/compression/xtc2.o build/temp.linux-arm64-cpython-311/mdtraj/formats/tng/src/compression/xtc3.o build/temp.linux-arm64-cpython-311/mdtraj/formats/tng/src/lib/md5.o build/temp.linux-arm64-cpython-311/mdtraj/formats/tng/src/lib/tng_io.o build/temp.linux-arm64-cpython-311/mdtraj/formats/tng/tng.o -L/usr/lib -L/usr/lib/aarch64-linux-gnu -lz -o /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/tng.cpython-311-aarch64-linux-gnu.so
building 'mdtraj.formats.dcd' extension
INFO: C compiler: aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC

INFO: compile options: '-Imdtraj/formats/dcd/include/ -Imdtraj/formats/dcd/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c'
extra options: '-Wno-unused-function -Wno-unreachable-code -Wno-sign-compare'
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/dcd/dcd.c
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/dcd/src/dcdplugin.c
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1940,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
                 from mdtraj/formats/dcd/dcd.c:776:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   17 | #warning "Using deprecated NumPy API, disable it with " \
      |  ^~~~~~~
mdtraj/formats/dcd/dcd.c: In function '__pyx_pf_6mdtraj_7formats_3dcd_17DCDTrajectoryFile_20read':
mdtraj/formats/dcd/dcd.c:688:40: warning: '__pyx_v_i' may be used uninitialized [-Wmaybe-uninitialized]
  688 |   #define PyInt_FromLong               PyLong_FromLong
      |                                        ^~~~~~~~~~~~~~~
mdtraj/formats/dcd/dcd.c:5434:7: note: '__pyx_v_i' was declared here
 5434 |   int __pyx_v_i;
      |       ^~~~~~~~~
INFO: aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-cpython-311/mdtraj/formats/dcd/dcd.o build/temp.linux-arm64-cpython-311/mdtraj/formats/dcd/src/dcdplugin.o -L/usr/lib/aarch64-linux-gnu -o /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/dcd.cpython-311-aarch64-linux-gnu.so
building 'mdtraj.formats.binpos' extension
INFO: C compiler: aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC

INFO: compile options: '-Imdtraj/formats/binpos/include/ -Imdtraj/formats/binpos/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c'
extra options: '-Wno-unused-function -Wno-unreachable-code -Wno-sign-compare'
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/binpos/binpos.c
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/binpos/src/binposplugin.c
mdtraj/formats/binpos/src/binposplugin.c: In function 'open_binpos_read':
mdtraj/formats/binpos/src/binposplugin.c:59:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
   59 |   fread(magicchar,sizeof(char),4,fd);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/binpos/src/binposplugin.c:69:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
   69 |   fread(&igarb,sizeof(int),1,fd);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1940,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
                 from mdtraj/formats/binpos/binpos.c:776:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   17 | #warning "Using deprecated NumPy API, disable it with " \
      |  ^~~~~~~
In function '__pyx_pf_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_8_read',
    inlined from '__pyx_pw_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_9_read' at mdtraj/formats/binpos/binpos.c:4980:13:
mdtraj/formats/binpos/binpos.c:5512:6: warning: '__pyx_v_status' may be used uninitialized [-Wmaybe-uninitialized]
 5512 |   if (__pyx_t_2) {
      |      ^
mdtraj/formats/binpos/binpos.c: In function '__pyx_pw_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_9_read':
mdtraj/formats/binpos/binpos.c:4992:7: note: '__pyx_v_status' was declared here
 4992 |   int __pyx_v_status;
      |       ^~~~~~~~~~~~~~
mdtraj/formats/binpos/binpos.c:688:40: warning: '__pyx_v_i' may be used uninitialized [-Wmaybe-uninitialized]
  688 |   #define PyInt_FromLong               PyLong_FromLong
      |                                        ^~~~~~~~~~~~~~~
mdtraj/formats/binpos/binpos.c:4989:7: note: '__pyx_v_i' was declared here
 4989 |   int __pyx_v_i;
      |       ^~~~~~~~~
INFO: aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-cpython-311/mdtraj/formats/binpos/binpos.o build/temp.linux-arm64-cpython-311/mdtraj/formats/binpos/src/binposplugin.o -L/usr/lib/aarch64-linux-gnu -o /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/binpos.cpython-311-aarch64-linux-gnu.so
building 'mdtraj.formats.dtr' extension
INFO: C compiler: aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC

INFO: compile options: '-DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c'
extra options: '-Wno-unused-function -Wno-unreachable-code -Wno-sign-compare'
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/dtr/dtr.cpp
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/dtr/src/dtrplugin.cxx
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1940,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
                 from mdtraj/formats/dtr/dtr.cpp:797:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   17 | #warning "Using deprecated NumPy API, disable it with " \
      |  ^~~~~~~
mdtraj/formats/dtr/src/dtrplugin.cxx: In member function 'bool desres::molfile::Timekeys::init(const std::string&)':
mdtraj/formats/dtr/src/dtrplugin.cxx: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 constructor '{anonymous}::DDException::DDException(const std::string&, int)':
mdtraj/formats/dtr/src/dtrplugin.cxx:680:43: warning: '*this.{anonymous}::DDException::eno' is used uninitialized [-Wuninitialized]
  680 |       : std::runtime_error(text + strerror(eno)), eno(_eno){}
      |                                   ~~~~~~~~^~~~~
mdtraj/formats/dtr/src/dtrplugin.cxx: In function 'void DDmkdir(const std::string&, mode_t, int, int)':
mdtraj/formats/dtr/src/dtrplugin.cxx:706:23: warning: '%03x' directive writing between 3 and 8 bytes into a region of size 6 [-Wformat-overflow=]
  706 |         sprintf(sub, "%03x/", i);
      |                       ^~~~
mdtraj/formats/dtr/src/dtrplugin.cxx:706:22: note: directive argument in the range [0, 2147483646]
  706 |         sprintf(sub, "%03x/", i);
      |                      ^~~~~~~
In file included from /usr/include/stdio.h:906,
                 from mdtraj/formats/dtr/include/molfile_plugin.h:35,
                 from mdtraj/formats/dtr/include/dtrplugin.hxx:46,
                 from mdtraj/formats/dtr/src/dtrplugin.cxx:42:
In function 'int sprintf(char*, const char*, ...)',
    inlined from 'void DDmkdir(const std::string&, mode_t, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:706:9:
/usr/include/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 ());
      |                                   ~~~~~~~~~~~~~~~~~
INFO: aarch64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-cpython-311/mdtraj/formats/dtr/dtr.o build/temp.linux-arm64-cpython-311/mdtraj/formats/dtr/src/dtrplugin.o -L/usr/lib/aarch64-linux-gnu -o /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/dtr.cpython-311-aarch64-linux-gnu.so
building 'mdtraj._rmsd' extension
INFO: C compiler: aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC

INFO: compile options: '-Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c'
extra options: '-fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare'
INFO: aarch64-linux-gnu-gcc: mdtraj/rmsd/_rmsd.cpp
INFO: aarch64-linux-gnu-gcc: mdtraj/rmsd/src/center.cpp
INFO: aarch64-linux-gnu-gcc: mdtraj/rmsd/src/rotation.cpp
INFO: aarch64-linux-gnu-gcc: mdtraj/rmsd/src/theobald_rmsd.cpp
INFO: aarch64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-cpython-311/mdtraj/rmsd/_rmsd.o build/temp.linux-arm64-cpython-311/mdtraj/rmsd/src/center.o build/temp.linux-arm64-cpython-311/mdtraj/rmsd/src/rotation.o build/temp.linux-arm64-cpython-311/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/_rmsd.cpython-311-aarch64-linux-gnu.so
building 'mdtraj._lprmsd' extension
INFO: C compiler: aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC

INFO: compile options: '-Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c'
extra options: '-fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare'
INFO: aarch64-linux-gnu-gcc: mdtraj/rmsd/_lprmsd.cpp
INFO: aarch64-linux-gnu-gcc: mdtraj/rmsd/src/Munkres.cpp
INFO: aarch64-linux-gnu-gcc: mdtraj/rmsd/src/center.cpp
INFO: aarch64-linux-gnu-gcc: mdtraj/rmsd/src/euclidean_permutation.cpp
INFO: aarch64-linux-gnu-gcc: mdtraj/rmsd/src/fancy_index.cpp
INFO: aarch64-linux-gnu-gcc: mdtraj/rmsd/src/rotation.cpp
INFO: aarch64-linux-gnu-gcc: mdtraj/rmsd/src/theobald_rmsd.cpp
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1940,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
                 from mdtraj/rmsd/_lprmsd.cpp:806:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   17 | #warning "Using deprecated NumPy API, disable it with " \
      |  ^~~~~~~
INFO: aarch64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-cpython-311/mdtraj/rmsd/_lprmsd.o build/temp.linux-arm64-cpython-311/mdtraj/rmsd/src/Munkres.o build/temp.linux-arm64-cpython-311/mdtraj/rmsd/src/center.o build/temp.linux-arm64-cpython-311/mdtraj/rmsd/src/euclidean_permutation.o build/temp.linux-arm64-cpython-311/mdtraj/rmsd/src/fancy_index.o build/temp.linux-arm64-cpython-311/mdtraj/rmsd/src/rotation.o build/temp.linux-arm64-cpython-311/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/_lprmsd.cpython-311-aarch64-linux-gnu.so
building 'mdtraj.geometry._geometry' extension
INFO: C compiler: aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC

INFO: compile options: '-Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c'
extra options: '-fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare'
INFO: aarch64-linux-gnu-gcc: mdtraj/geometry/src/_geometry.cpp
INFO: aarch64-linux-gnu-gcc: mdtraj/geometry/src/dssp.cpp
INFO: aarch64-linux-gnu-gcc: mdtraj/geometry/src/geometry.cpp
INFO: aarch64-linux-gnu-gcc: mdtraj/geometry/src/sasa.cpp
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1940,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
                 from mdtraj/geometry/src/_geometry.cpp:808:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   17 | #warning "Using deprecated NumPy API, disable it with " \
      |  ^~~~~~~
mdtraj/geometry/src/_geometry.cpp: In function 'void __pyx_f_6mdtraj_8geometry_9_geometry_make_whole(__Pyx_memviewslice, __Pyx_memviewslice, __Pyx_memviewslice)':
mdtraj/geometry/src/_geometry.cpp:6084:224: warning: '__pyx_v_delta[2]' may be used uninitialized [-Wmaybe-uninitialized]
 6084 |       (__pyx_v_offset[__pyx_v_k]) = ((*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_frame_unitcell_vectors.data + __pyx_t_8 * __pyx_v_frame_unitcell_vectors.strides[0]) )) + __pyx_t_7)) ))) * roundf(((__pyx_v_delta[2]) / (*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_frame_unitcell_vectors.data + __pyx_t_5 * __pyx_v_frame_unitcell_vectors.strides[0]) )) + __pyx_t_4)) ))))));
      |                                                                                                                                                                                                                          ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/geometry/src/_geometry.cpp:6005:9: note: '__pyx_v_delta[2]' was declared here
 6005 |   float __pyx_v_delta[3];
      |         ^~~~~~~~~~~~~
mdtraj/geometry/src/_geometry.cpp:6098:277: warning: '__pyx_v_delta[1]' may be used uninitialized [-Wmaybe-uninitialized]
 6098 |       (__pyx_v_offset[__pyx_t_9]) = ((__pyx_v_offset[__pyx_t_9]) + ((*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_frame_unitcell_vectors.data + __pyx_t_4 * __pyx_v_frame_unitcell_vectors.strides[0]) )) + __pyx_t_5)) ))) * roundf((((__pyx_v_delta[1]) - (__pyx_v_offset[1])) / (*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_frame_unitcell_vectors.data + __pyx_t_7 * __pyx_v_frame_unitcell_vectors.strides[0]) )) + __pyx_t_8)) )))))));
      |                                                                                                                                                                                                                                                                 ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
mdtraj/geometry/src/_geometry.cpp:6005:9: note: '__pyx_v_delta[1]' was declared here
 6005 |   float __pyx_v_delta[3];
      |         ^~~~~~~~~~~~~
mdtraj/geometry/src/_geometry.cpp:6098:277: warning: '__pyx_v_offset[1]' may be used uninitialized [-Wmaybe-uninitialized]
 6098 |       (__pyx_v_offset[__pyx_t_9]) = ((__pyx_v_offset[__pyx_t_9]) + ((*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_frame_unitcell_vectors.data + __pyx_t_4 * __pyx_v_frame_unitcell_vectors.strides[0]) )) + __pyx_t_5)) ))) * roundf((((__pyx_v_delta[1]) - (__pyx_v_offset[1])) / (*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_frame_unitcell_vectors.data + __pyx_t_7 * __pyx_v_frame_unitcell_vectors.strides[0]) )) + __pyx_t_8)) )))))));
      |                                                                                                                                                                                                                                                                 ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
mdtraj/geometry/src/_geometry.cpp:6004:9: note: '__pyx_v_offset[1]' was declared here
 6004 |   float __pyx_v_offset[3];
      |         ^~~~~~~~~~~~~~
INFO: aarch64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-cpython-311/mdtraj/geometry/src/_geometry.o build/temp.linux-arm64-cpython-311/mdtraj/geometry/src/dssp.o build/temp.linux-arm64-cpython-311/mdtraj/geometry/src/geometry.o build/temp.linux-arm64-cpython-311/mdtraj/geometry/src/sasa.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/_geometry.cpython-311-aarch64-linux-gnu.so
building 'mdtraj.geometry.drid' extension
INFO: C compiler: aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC

INFO: compile options: '-Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c'
extra options: '-fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare'
INFO: aarch64-linux-gnu-gcc: mdtraj/geometry/drid.cpp
INFO: aarch64-linux-gnu-gcc: mdtraj/geometry/src/dridkernels.cpp
INFO: aarch64-linux-gnu-gcc: mdtraj/geometry/src/moments.cpp
INFO: aarch64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-cpython-311/mdtraj/geometry/drid.o build/temp.linux-arm64-cpython-311/mdtraj/geometry/src/dridkernels.o build/temp.linux-arm64-cpython-311/mdtraj/geometry/src/moments.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/drid.cpython-311-aarch64-linux-gnu.so
building 'mdtraj.geometry.neighbors' extension
INFO: C compiler: aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC

INFO: compile options: '-Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c'
extra options: '-fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare'
INFO: aarch64-linux-gnu-gcc: mdtraj/geometry/neighbors.cpp
INFO: aarch64-linux-gnu-gcc: mdtraj/geometry/src/neighbors.cpp
INFO: aarch64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-cpython-311/mdtraj/geometry/neighbors.o build/temp.linux-arm64-cpython-311/mdtraj/geometry/src/neighbors.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/neighbors.cpython-311-aarch64-linux-gnu.so
building 'mdtraj.geometry.neighborlist' extension
INFO: C compiler: aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC

INFO: compile options: '-Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c'
extra options: '-fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare'
INFO: aarch64-linux-gnu-gcc: mdtraj/geometry/neighborlist.cpp
INFO: aarch64-linux-gnu-gcc: mdtraj/geometry/src/neighborlist.cpp
In constructor 'Voxels::Voxels(float, float, float, float, float, float, const float (&)[3][3], bool)',
    inlined from 'std::vector<std::vector<int> > _compute_neighborlist(const float*, int, float, const float*)' at mdtraj/geometry/src/neighborlist.cpp:377:116:
mdtraj/geometry/src/neighborlist.cpp:50:53: warning: 'periodicBoxVectors' may be used uninitialized [-Wmaybe-uninitialized]
   50 |         periodicBoxSize[0] = periodicBoxVectors[0][0];
      |                              ~~~~~~~~~~~~~~~~~~~~~~~^
mdtraj/geometry/src/neighborlist.cpp: In function 'std::vector<std::vector<int> > _compute_neighborlist(const float*, int, float, const float*)':
mdtraj/geometry/src/neighborlist.cpp:341:11: note: 'periodicBoxVectors' declared here
  341 |     float periodicBoxVectors[3][3];
      |           ^~~~~~~~~~~~~~~~~~
In constructor 'Voxels::Voxels(float, float, float, float, float, float, const float (&)[3][3], bool)',
    inlined from 'std::vector<std::vector<int> > _compute_neighborlist(const float*, int, float, const float*)' at mdtraj/geometry/src/neighborlist.cpp:377:116:
mdtraj/geometry/src/neighborlist.cpp:51:53: warning: 'periodicBoxVectors' may be used uninitialized [-Wmaybe-uninitialized]
   51 |         periodicBoxSize[1] = periodicBoxVectors[1][1];
      |                              ~~~~~~~~~~~~~~~~~~~~~~~^
mdtraj/geometry/src/neighborlist.cpp: In function 'std::vector<std::vector<int> > _compute_neighborlist(const float*, int, float, const float*)':
mdtraj/geometry/src/neighborlist.cpp:341:11: note: 'periodicBoxVectors' declared here
  341 |     float periodicBoxVectors[3][3];
      |           ^~~~~~~~~~~~~~~~~~
In constructor 'Voxels::Voxels(float, float, float, float, float, float, const float (&)[3][3], bool)',
    inlined from 'std::vector<std::vector<int> > _compute_neighborlist(const float*, int, float, const float*)' at mdtraj/geometry/src/neighborlist.cpp:377:116:
mdtraj/geometry/src/neighborlist.cpp:52:53: warning: 'periodicBoxVectors' may be used uninitialized [-Wmaybe-uninitialized]
   52 |         periodicBoxSize[2] = periodicBoxVectors[2][2];
      |                              ~~~~~~~~~~~~~~~~~~~~~~~^
mdtraj/geometry/src/neighborlist.cpp: In function 'std::vector<std::vector<int> > _compute_neighborlist(const float*, int, float, const float*)':
mdtraj/geometry/src/neighborlist.cpp:341:11: note: 'periodicBoxVectors' declared here
  341 |     float periodicBoxVectors[3][3];
      |           ^~~~~~~~~~~~~~~~~~
In constructor 'Voxels::Voxels(float, float, float, float, float, float, const float (&)[3][3], bool)',
    inlined from 'std::vector<std::vector<int> > _compute_neighborlist(const float*, int, float, const float*)' at mdtraj/geometry/src/neighborlist.cpp:377:116:
mdtraj/geometry/src/neighborlist.cpp:56:45: warning: 'periodicBoxVectors' may be used uninitialized [-Wmaybe-uninitialized]
   56 |         triclinic = (periodicBoxVectors[0][1] != 0.0 || periodicBoxVectors[0][2] != 0.0 ||
      |                      ~~~~~~~~~~~~~~~~~~~~~~~^
mdtraj/geometry/src/neighborlist.cpp: In function 'std::vector<std::vector<int> > _compute_neighborlist(const float*, int, float, const float*)':
mdtraj/geometry/src/neighborlist.cpp:341:11: note: 'periodicBoxVectors' declared here
  341 |     float periodicBoxVectors[3][3];
      |           ^~~~~~~~~~~~~~~~~~
INFO: aarch64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-cpython-311/mdtraj/geometry/neighborlist.o build/temp.linux-arm64-cpython-311/mdtraj/geometry/src/neighborlist.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/neighborlist.cpython-311-aarch64-linux-gnu.so
   dh_auto_test -O--buildsystem=pybuild
I: pybuild base:240: cd /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build; python3.11 -m unittest discover -v 

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

OK
   create-stamp debian/debhelper-build-stamp
 fakeroot debian/rules binary
dh binary --with python3,sphinxdoc --buildsystem=pybuild
   dh_testroot -O--buildsystem=pybuild
   dh_prep -O--buildsystem=pybuild
   dh_installdirs -O--buildsystem=pybuild
   dh_auto_install -O--buildsystem=pybuild
I: pybuild base:240: /usr/bin/python3 setup.py install --root /build/mdtraj-1.9.7/debian/python3-mdtraj 
Using built-in specs.
COLLECT_GCC=/usr/bin/aarch64-linux-gnu-gcc
COLLECT_LTO_WRAPPER=/usr/lib/gcc/aarch64-linux-gnu/12/lto-wrapper
Target: aarch64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Debian 12.2.0-14' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=aarch64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-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-checking=release --build=aarch64-linux-gnu --host=aarch64-linux-gnu --target=aarch64-linux-gnu
Thread model: posix
Supported LTO compression algorithms: zlib zstd
gcc version 12.2.0 (Debian 12.2.0-14) 
/usr/lib/python3/dist-packages/pythran/tables.py:4530: FutureWarning: In the future `np.bool` will be defined as the corresponding NumPy scalar.
  if not hasattr(numpy, method):
/usr/lib/python3/dist-packages/pythran/tables.py:4563: FutureWarning: In the future `np.bytes` will be defined as the corresponding NumPy scalar.
  obj = getattr(themodule, elem)
warning: mdtraj/formats/dcd/dcdlib.pxd:12:12: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: mdtraj/formats/dcd/dcdlib.pxd:12:16: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: mdtraj/formats/dcd/dcdlib.pxd:12:20: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
C compiler:
Attempting to autodetect OpenMP support... Compiler supports OpenMP
Attempting to autodetect SSE3   support... 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

[ 1/12] Cythonizing mdtraj/formats/binpos/binpos.pyx
[ 2/12] Cythonizing mdtraj/formats/dcd/dcd.pyx
[ 3/12] Cythonizing mdtraj/formats/dtr/dtr.pyx
[ 4/12] Cythonizing mdtraj/formats/tng/tng.pyx
[ 5/12] Cythonizing mdtraj/formats/xtc/trr.pyx
[ 6/12] Cythonizing mdtraj/formats/xtc/xtc.pyx
[ 7/12] Cythonizing mdtraj/geometry/drid.pyx
[ 8/12] Cythonizing mdtraj/geometry/neighborlist.pyx
[ 9/12] Cythonizing mdtraj/geometry/neighbors.pyx
[10/12] Cythonizing mdtraj/geometry/src/_geometry.pyx
[11/12] Cythonizing mdtraj/rmsd/_lprmsd.pyx
[12/12] Cythonizing mdtraj/rmsd/_rmsd.pyx
running install
/usr/lib/python3/dist-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
  warnings.warn(
running build
running build_py
copying mdtraj/version.py -> /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj
running build_ext
building 'mdtraj.formats.xtc' extension
INFO: C compiler: aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC

INFO: compile options: '-Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c'
extra options: '-Wno-unused-function -Wno-unreachable-code -Wno-sign-compare'
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/xtc/src/xdr_seek.c
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/xtc/src/xdrfile.c
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/xtc/src/xdrfile_xtc.c
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/xtc/xtc.c
mdtraj/formats/xtc/src/xdrfile_xtc.c: In function 'xtc_coord':
mdtraj/formats/xtc/src/xdrfile_xtc.c:66:15: warning: unused variable 'j' [-Wunused-variable]
   66 |         int i,j,result;
      |               ^
mdtraj/formats/xtc/src/xdrfile_xtc.c:66:13: warning: unused variable 'i' [-Wunused-variable]
   66 |         int i,j,result;
      |             ^
mdtraj/formats/xtc/src/xdrfile_xtc.c: In function 'read_xtc_nframes':
mdtraj/formats/xtc/src/xdrfile_xtc.c:119:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  119 |     if (NULL == xd)
      |     ^~
mdtraj/formats/xtc/src/xdrfile_xtc.c:122:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  122 |         do {
      |         ^~
mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_decompress_coord_float':
mdtraj/formats/xtc/src/xdrfile.c:788:32: warning: variable 'larger' set but not used [-Wunused-but-set-variable]
  788 |         int smallnum, smaller, larger, i, is_smaller, run;
      |                                ^~~~~~
mdtraj/formats/xtc/src/xdrfile.c:785:23: warning: variable 'minidx' set but not used [-Wunused-but-set-variable]
  785 |         int smallidx, minidx, maxidx;
      |                       ^~~~~~
mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_compress_coord_float':
mdtraj/formats/xtc/src/xdrfile.c:1016:13: warning: variable 'errval' set but not used [-Wunused-but-set-variable]
 1016 |         int errval=1;
      |             ^~~~~~
mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_decompress_coord_double':
mdtraj/formats/xtc/src/xdrfile.c:1305:32: warning: variable 'larger' set but not used [-Wunused-but-set-variable]
 1305 |         int smallnum, smaller, larger, i, is_smaller, run;
      |                                ^~~~~~
mdtraj/formats/xtc/src/xdrfile.c:1302:23: warning: variable 'minidx' set but not used [-Wunused-but-set-variable]
 1302 |         int smallidx, minidx, maxidx;
      |                       ^~~~~~
mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_compress_coord_double':
mdtraj/formats/xtc/src/xdrfile.c:1509:13: warning: variable 'errval' set but not used [-Wunused-but-set-variable]
 1509 |         int errval=1;
      |             ^~~~~~
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1940,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
                 from mdtraj/formats/xtc/xtc.c:778:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   17 | #warning "Using deprecated NumPy API, disable it with " \
      |  ^~~~~~~
mdtraj/formats/xtc/xtc.c: In function '__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_16_write':
mdtraj/formats/xtc/xtc.c:690:40: warning: '__pyx_v_status' may be used uninitialized [-Wmaybe-uninitialized]
  690 |   #define PyInt_FromLong               PyLong_FromLong
      |                                        ^~~~~~~~~~~~~~~
mdtraj/formats/xtc/xtc.c:9539:7: note: '__pyx_v_status' was declared here
 9539 |   int __pyx_v_status;
      |       ^~~~~~~~~~~~~~
mdtraj/formats/xtc/xtc.c: In function '__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_12_read':
mdtraj/formats/xtc/xtc.c:8058:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized]
 8058 |             } else if (unlikely(__pyx_t_39 >= __pyx_pybuffernd_xyz_stride.diminfo[2].shape)) __pyx_t_6 = 2;
      |                       ^
mdtraj/formats/xtc/xtc.c:6461:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[2].shape' was declared here
 6461 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/xtc.c:8054:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized]
 8054 |             } else if (unlikely(__pyx_t_38 >= __pyx_pybuffernd_xyz_stride.diminfo[1].shape)) __pyx_t_6 = 1;
      |                       ^
mdtraj/formats/xtc/xtc.c:6461:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[1].shape' was declared here
 6461 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/xtc.c:8050:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized]
 8050 |             } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_xyz_stride.diminfo[0].shape)) __pyx_t_6 = 0;
      |                       ^
mdtraj/formats/xtc/xtc.c:6461:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[0].shape' was declared here
 6461 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/xtc.c:8010:23: warning: '__pyx_pybuffernd_time_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized]
 8010 |             } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_time_stride.diminfo[0].shape)) __pyx_t_6 = 0;
      |                       ^
mdtraj/formats/xtc/xtc.c:6457:21: note: '__pyx_pybuffernd_time_stride.diminfo[0].shape' was declared here
 6457 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_time_stride;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/xtc.c:7992:23: warning: '__pyx_pybuffernd_step_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized]
 7992 |             } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_step_stride.diminfo[0].shape)) __pyx_t_6 = 0;
      |                       ^
mdtraj/formats/xtc/xtc.c:6453:21: note: '__pyx_pybuffernd_step_stride.diminfo[0].shape' was declared here
 6453 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_step_stride;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/xtc.c:8068:23: warning: '__pyx_pybuffernd_prec_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized]
 8068 |             } else if (unlikely(__pyx_t_40 >= __pyx_pybuffernd_prec_stride.diminfo[0].shape)) __pyx_t_6 = 0;
      |                       ^
mdtraj/formats/xtc/xtc.c:6449:21: note: '__pyx_pybuffernd_prec_stride.diminfo[0].shape' was declared here
 6449 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_prec_stride;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/xtc.c:8030:23: warning: '__pyx_pybuffernd_box_stride.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized]
 8030 |             } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_box_stride.diminfo[2].shape)) __pyx_t_6 = 2;
      |                       ^
mdtraj/formats/xtc/xtc.c:6443:21: note: '__pyx_pybuffernd_box_stride.diminfo[2].shape' was declared here
 6443 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/xtc.c:8026:23: warning: '__pyx_pybuffernd_box_stride.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized]
 8026 |             } else if (unlikely(__pyx_t_33 >= __pyx_pybuffernd_box_stride.diminfo[1].shape)) __pyx_t_6 = 1;
      |                       ^
mdtraj/formats/xtc/xtc.c:6443:21: note: '__pyx_pybuffernd_box_stride.diminfo[1].shape' was declared here
 6443 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/xtc.c:8022:23: warning: '__pyx_pybuffernd_box_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized]
 8022 |             } else if (unlikely(__pyx_t_32 >= __pyx_pybuffernd_box_stride.diminfo[0].shape)) __pyx_t_6 = 0;
      |                       ^
mdtraj/formats/xtc/xtc.c:6443:21: note: '__pyx_pybuffernd_box_stride.diminfo[0].shape' was declared here
 6443 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/xtc.c:7645:17: warning: '__pyx_pybuffernd_framebuffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized]
 7645 |       } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_framebuffer.diminfo[1].shape)) __pyx_t_6 = 1;
      |                 ^
mdtraj/formats/xtc/xtc.c:6445:21: note: '__pyx_pybuffernd_framebuffer.diminfo[1].shape' was declared here
 6445 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_framebuffer;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/xtc.c:7641:17: warning: '__pyx_pybuffernd_framebuffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized]
 7641 |       } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_framebuffer.diminfo[0].shape)) __pyx_t_6 = 0;
      |                 ^
mdtraj/formats/xtc/xtc.c:6445:21: note: '__pyx_pybuffernd_framebuffer.diminfo[0].shape' was declared here
 6445 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_framebuffer;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
INFO: aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-cpython-311/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-arm64-cpython-311/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-arm64-cpython-311/mdtraj/formats/xtc/src/xdrfile_xtc.o build/temp.linux-arm64-cpython-311/mdtraj/formats/xtc/xtc.o -L/usr/lib/aarch64-linux-gnu -o /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/xtc.cpython-311-aarch64-linux-gnu.so
building 'mdtraj.formats.trr' extension
INFO: C compiler: aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC

INFO: compile options: '-Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c'
extra options: '-Wno-unused-function -Wno-unreachable-code -Wno-sign-compare'
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/xtc/src/xdr_seek.c
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/xtc/src/xdrfile.c
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/xtc/src/xdrfile_trr.c
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/xtc/trr.c
mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_decompress_coord_float':
mdtraj/formats/xtc/src/xdrfile.c:788:32: warning: variable 'larger' set but not used [-Wunused-but-set-variable]
  788 |         int smallnum, smaller, larger, i, is_smaller, run;
      |                                ^~~~~~
mdtraj/formats/xtc/src/xdrfile.c:785:23: warning: variable 'minidx' set but not used [-Wunused-but-set-variable]
  785 |         int smallidx, minidx, maxidx;
      |                       ^~~~~~
mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_compress_coord_float':
mdtraj/formats/xtc/src/xdrfile.c:1016:13: warning: variable 'errval' set but not used [-Wunused-but-set-variable]
 1016 |         int errval=1;
      |             ^~~~~~
mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_decompress_coord_double':
mdtraj/formats/xtc/src/xdrfile.c:1305:32: warning: variable 'larger' set but not used [-Wunused-but-set-variable]
 1305 |         int smallnum, smaller, larger, i, is_smaller, run;
      |                                ^~~~~~
mdtraj/formats/xtc/src/xdrfile.c:1302:23: warning: variable 'minidx' set but not used [-Wunused-but-set-variable]
 1302 |         int smallidx, minidx, maxidx;
      |                       ^~~~~~
mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_compress_coord_double':
mdtraj/formats/xtc/src/xdrfile.c:1509:13: warning: variable 'errval' set but not used [-Wunused-but-set-variable]
 1509 |         int errval=1;
      |             ^~~~~~
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1940,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
                 from mdtraj/formats/xtc/trr.c:778:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   17 | #warning "Using deprecated NumPy API, disable it with " \
      |  ^~~~~~~
mdtraj/formats/xtc/trr.c: In function '__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_18_write':
mdtraj/formats/xtc/trr.c:690:40: warning: '__pyx_v_status' may be used uninitialized [-Wmaybe-uninitialized]
  690 |   #define PyInt_FromLong               PyLong_FromLong
      |                                        ^~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:11065:7: note: '__pyx_v_status' was declared here
11065 |   int __pyx_v_status;
      |       ^~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c: In function '__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_14_read':
mdtraj/formats/xtc/trr.c:8418:19: warning: '__pyx_pybuffernd_forces.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized]
 8418 |         } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_forces.diminfo[2].shape)) __pyx_t_5 = 2;
      |                   ^
mdtraj/formats/xtc/trr.c:6955:21: note: '__pyx_pybuffernd_forces.diminfo[2].shape' was declared here
 6955 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_forces;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:8414:19: warning: '__pyx_pybuffernd_forces.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized]
 8414 |         } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_forces.diminfo[1].shape)) __pyx_t_5 = 1;
      |                   ^
mdtraj/formats/xtc/trr.c:6955:21: note: '__pyx_pybuffernd_forces.diminfo[1].shape' was declared here
 6955 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_forces;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:1929:90: warning: '__pyx_pybuffernd_forces.diminfo[0].strides' may be used uninitialized [-Wmaybe-uninitialized]
 1929 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2)
      |                                                                                          ^
mdtraj/formats/xtc/trr.c:6955:21: note: '__pyx_pybuffernd_forces.diminfo[0].strides' was declared here
 6955 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_forces;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:8410:19: warning: '__pyx_pybuffernd_forces.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized]
 8410 |         } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_forces.diminfo[0].shape)) __pyx_t_5 = 0;
      |                   ^
mdtraj/formats/xtc/trr.c:6955:21: note: '__pyx_pybuffernd_forces.diminfo[0].shape' was declared here
 6955 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_forces;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:8361:19: warning: '__pyx_pybuffernd_vel.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized]
 8361 |         } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_vel.diminfo[2].shape)) __pyx_t_5 = 2;
      |                   ^
mdtraj/formats/xtc/trr.c:6971:21: note: '__pyx_pybuffernd_vel.diminfo[2].shape' was declared here
 6971 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_vel;
      |                     ^~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:8357:19: warning: '__pyx_pybuffernd_vel.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized]
 8357 |         } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_vel.diminfo[1].shape)) __pyx_t_5 = 1;
      |                   ^
mdtraj/formats/xtc/trr.c:6971:21: note: '__pyx_pybuffernd_vel.diminfo[1].shape' was declared here
 6971 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_vel;
      |                     ^~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:1929:90: warning: '__pyx_pybuffernd_vel.diminfo[0].strides' may be used uninitialized [-Wmaybe-uninitialized]
 1929 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2)
      |                                                                                          ^
mdtraj/formats/xtc/trr.c:6971:21: note: '__pyx_pybuffernd_vel.diminfo[0].strides' was declared here
 6971 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_vel;
      |                     ^~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:8353:19: warning: '__pyx_pybuffernd_vel.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized]
 8353 |         } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_vel.diminfo[0].shape)) __pyx_t_5 = 0;
      |                   ^
mdtraj/formats/xtc/trr.c:6971:21: note: '__pyx_pybuffernd_vel.diminfo[0].shape' was declared here
 6971 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_vel;
      |                     ^~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:8751:17: warning: '__pyx_pybuffernd_xyz_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized]
 8751 |       } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_xyz_buffer.diminfo[1].shape)) __pyx_t_5 = 1;
      |                 ^
mdtraj/formats/xtc/trr.c:6977:21: note: '__pyx_pybuffernd_xyz_buffer.diminfo[1].shape' was declared here
 6977 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:8747:17: warning: '__pyx_pybuffernd_xyz_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized]
 8747 |       } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_xyz_buffer.diminfo[0].shape)) __pyx_t_5 = 0;
      |                 ^
mdtraj/formats/xtc/trr.c:6977:21: note: '__pyx_pybuffernd_xyz_buffer.diminfo[0].shape' was declared here
 6977 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:8592:19: warning: '__pyx_pybuffernd_vel_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized]
 8592 |         } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_vel_buffer.diminfo[1].shape)) __pyx_t_5 = 1;
      |                   ^
mdtraj/formats/xtc/trr.c:6973:21: note: '__pyx_pybuffernd_vel_buffer.diminfo[1].shape' was declared here
 6973 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:8588:19: warning: '__pyx_pybuffernd_vel_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized]
 8588 |         } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_vel_buffer.diminfo[0].shape)) __pyx_t_5 = 0;
      |                   ^
mdtraj/formats/xtc/trr.c:6973:21: note: '__pyx_pybuffernd_vel_buffer.diminfo[0].shape' was declared here
 6973 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:8644:19: warning: '__pyx_pybuffernd_forces_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized]
 8644 |         } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_forces_buffer.diminfo[1].shape)) __pyx_t_5 = 1;
      |                   ^
mdtraj/formats/xtc/trr.c:6957:21: note: '__pyx_pybuffernd_forces_buffer.diminfo[1].shape' was declared here
 6957 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_forces_buffer;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:8640:19: warning: '__pyx_pybuffernd_forces_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized]
 8640 |         } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_forces_buffer.diminfo[0].shape)) __pyx_t_5 = 0;
      |                   ^
mdtraj/formats/xtc/trr.c:6957:21: note: '__pyx_pybuffernd_forces_buffer.diminfo[0].shape' was declared here
 6957 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_forces_buffer;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
INFO: aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-cpython-311/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-arm64-cpython-311/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-arm64-cpython-311/mdtraj/formats/xtc/src/xdrfile_trr.o build/temp.linux-arm64-cpython-311/mdtraj/formats/xtc/trr.o -L/usr/lib/aarch64-linux-gnu -o /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/trr.cpython-311-aarch64-linux-gnu.so
building 'mdtraj.formats.tng' extension
INFO: C compiler: aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC

INFO: compile options: '-DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c'
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/tng/src/compression/bwlzh.c
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/tng/src/compression/bwt.c
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/tng/src/compression/coder.c
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/tng/src/compression/dict.c
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/tng/src/compression/fixpoint.c
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/tng/src/compression/huffman.c
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/tng/src/compression/huffmem.c
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/tng/src/compression/lz77.c
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/tng/src/compression/merge_sort.c
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/tng/src/compression/mtf.c
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/tng/src/compression/rle.c
mdtraj/formats/tng/src/compression/mtf.c: In function 'Ptngc_comp_conv_to_mtf':
mdtraj/formats/tng/src/compression/mtf.c:196:23: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
  196 |       while (dict[ptr]!=v)
      |                       ^~
mdtraj/formats/tng/src/compression/rle.c: In function 'Ptngc_comp_conv_to_rle':
mdtraj/formats/tng/src/compression/rle.c:56:16: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
   56 |           if (v==vals[i])
      |                ^~
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/tng/src/compression/tng_compress.c
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/tng/src/compression/vals16.c
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/tng/src/compression/warnmalloc.c
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/tng/src/compression/widemuldiv.c
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/tng/src/compression/xtc2.c
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/tng/src/compression/xtc3.c
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/tng/src/lib/md5.c
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/tng/src/lib/tng_io.c
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/tng/tng.c
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_block_header_read':
mdtraj/formats/tng/src/lib/tng_io.c:1064:57: warning: assignment to 'tng_function_status (*)(struct tng_trajectory * const,  int32_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const,  int *)'} from incompatible pointer type 'tng_function_status (*)(struct tng_trajectory * const,  uint32_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const,  unsigned int *)'} [-Wincompatible-pointer-types]
 1064 |                 tng_data->input_endianness_swap_func_32 =
      |                                                         ^
mdtraj/formats/tng/src/lib/tng_io.c:1073:57: warning: assignment to 'tng_function_status (*)(struct tng_trajectory * const,  int64_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const,  long int *)'} from incompatible pointer type 'tng_function_status (*)(struct tng_trajectory * const,  uint64_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const,  long unsigned int *)'} [-Wincompatible-pointer-types]
 1073 |                 tng_data->input_endianness_swap_func_64 =
      |                                                         ^
mdtraj/formats/tng/src/lib/tng_io.c:1089:57: warning: assignment to 'tng_function_status (*)(struct tng_trajectory * const,  int32_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const,  int *)'} from incompatible pointer type 'tng_function_status (*)(struct tng_trajectory * const,  uint32_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const,  unsigned int *)'} [-Wincompatible-pointer-types]
 1089 |                 tng_data->input_endianness_swap_func_32 =
      |                                                         ^
mdtraj/formats/tng/src/lib/tng_io.c:1098:57: warning: assignment to 'tng_function_status (*)(struct tng_trajectory * const,  int64_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const,  long int *)'} from incompatible pointer type 'tng_function_status (*)(struct tng_trajectory * const,  uint64_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const,  long unsigned int *)'} [-Wincompatible-pointer-types]
 1098 |                 tng_data->input_endianness_swap_func_64 =
      |                                                         ^
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_output_file_endianness_get':
mdtraj/formats/tng/src/lib/tng_io.c:9565:53: warning: comparison of distinct pointer types lacks a cast
 9565 |         if(tng_data->output_endianness_swap_func_32 ==
      |                                                     ^~
mdtraj/formats/tng/src/lib/tng_io.c:9570:58: warning: comparison of distinct pointer types lacks a cast
 9570 |         else if(tng_data->output_endianness_swap_func_32 ==
      |                                                          ^~
mdtraj/formats/tng/src/lib/tng_io.c:9588:53: warning: comparison of distinct pointer types lacks a cast
 9588 |         if(tng_data->output_endianness_swap_func_64 ==
      |                                                     ^~
mdtraj/formats/tng/src/lib/tng_io.c:9593:58: warning: comparison of distinct pointer types lacks a cast
 9593 |         else if(tng_data->output_endianness_swap_func_64 ==
      |                                                          ^~
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_output_file_endianness_set':
mdtraj/formats/tng/src/lib/tng_io.c:9651:54: warning: assignment to 'tng_function_status (*)(struct tng_trajectory * const,  int32_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const,  int *)'} from incompatible pointer type 'tng_function_status (*)(struct tng_trajectory * const,  uint32_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const,  unsigned int *)'} [-Wincompatible-pointer-types]
 9651 |             tng_data->output_endianness_swap_func_32 =
      |                                                      ^
mdtraj/formats/tng/src/lib/tng_io.c:9660:54: warning: assignment to 'tng_function_status (*)(struct tng_trajectory * const,  int64_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const,  long int *)'} from incompatible pointer type 'tng_function_status (*)(struct tng_trajectory * const,  uint64_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const,  long unsigned int *)'} [-Wincompatible-pointer-types]
 9660 |             tng_data->output_endianness_swap_func_64 =
      |                                                      ^
mdtraj/formats/tng/src/lib/tng_io.c:9673:54: warning: assignment to 'tng_function_status (*)(struct tng_trajectory * const,  int32_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const,  int *)'} from incompatible pointer type 'tng_function_status (*)(struct tng_trajectory * const,  uint32_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const,  unsigned int *)'} [-Wincompatible-pointer-types]
 9673 |             tng_data->output_endianness_swap_func_32 =
      |                                                      ^
mdtraj/formats/tng/src/lib/tng_io.c:9682:54: warning: assignment to 'tng_function_status (*)(struct tng_trajectory * const,  int64_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const,  long int *)'} from incompatible pointer type 'tng_function_status (*)(struct tng_trajectory * const,  uint64_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const,  long unsigned int *)'} [-Wincompatible-pointer-types]
 9682 |             tng_data->output_endianness_swap_func_64 =
      |                                                      ^
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1940,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
                 from mdtraj/formats/tng/tng.c:804:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   17 | #warning "Using deprecated NumPy API, disable it with " \
      |  ^~~~~~~
mdtraj/formats/tng/tng.c: In function '__pyx_pf_6mdtraj_7formats_3tng_17TNGTrajectoryFile___cinit__':
mdtraj/formats/tng/tng.c:3692:104: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare]
 3692 |   __pyx_t_1 = ((tng_util_trajectory_open(__pyx_v_filename, __pyx_v_self->mode, (&__pyx_v_self->_traj)) == __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
      |                                                                                                        ^~
mdtraj/formats/tng/tng.c:3747:88: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare]
 3747 |     __pyx_t_1 = ((tng_num_particles_get(__pyx_v_self->_traj, (&__pyx_v_self->n_atoms)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
      |                                                                                        ^~
mdtraj/formats/tng/tng.c:3779:90: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare]
 3779 |     __pyx_t_1 = ((tng_num_frames_get(__pyx_v_self->_traj, (&__pyx_v_self->tot_n_frames)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
      |                                                                                          ^~
mdtraj/formats/tng/tng.c:3811:95: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare]
 3811 |     __pyx_t_1 = ((tng_distance_unit_exponential_get(__pyx_v_self->_traj, (&__pyx_v_exponent)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
      |                                                                                               ^~
mdtraj/formats/tng/tng.c:3881:113: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare]
 3881 |     __pyx_t_1 = ((tng_num_frames_per_frame_set_get(__pyx_v_self->_traj, (&__pyx_v_self->_frames_per_frame_set)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
      |                                                                                                                 ^~
mdtraj/formats/tng/tng.c:3925:77: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare]
 3925 |     __pyx_t_1 = ((tng_last_program_name_set(__pyx_v_self->_traj, __pyx_t_8) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
      |                                                                             ^~
mdtraj/formats/tng/tng.c: In function '__pyx_pf_6mdtraj_7formats_3tng_17TNGTrajectoryFile_8_read_topology':
mdtraj/formats/tng/tng.c:4721:106: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare]
 4721 |     __pyx_t_7 = ((tng_chain_name_of_particle_nr_get(__pyx_v_self->_traj, __pyx_v_i, __pyx_v_text, 0x400) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
      |                                                                                                          ^~
mdtraj/formats/tng/tng.c:4766:108: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare]
 4766 |     __pyx_t_7 = ((tng_residue_name_of_particle_nr_get(__pyx_v_self->_traj, __pyx_v_i, __pyx_v_text, 0x400) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
      |                                                                                                            ^~
mdtraj/formats/tng/tng.c:4873:115: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare]
 4873 |     __pyx_t_8 = ((tng_global_residue_id_of_particle_nr_get(__pyx_v_self->_traj, __pyx_v_i, (&__pyx_v_residue_id)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
      |                                                                                                                   ^~
mdtraj/formats/tng/tng.c:4903:105: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare]
 4903 |     __pyx_t_8 = ((tng_atom_name_of_particle_nr_get(__pyx_v_self->_traj, __pyx_v_i, __pyx_v_text, 0x400) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
      |                                                                                                         ^~
mdtraj/formats/tng/tng.c:5031:105: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare]
 5031 |     __pyx_t_8 = ((tng_atom_type_of_particle_nr_get(__pyx_v_self->_traj, __pyx_v_i, __pyx_v_text, 0x400) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
      |                                                                                                         ^~
mdtraj/formats/tng/tng.c:5632:126: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare]
 5632 |   __pyx_t_7 = ((tng_molsystem_bonds_get(__pyx_v_self->_traj, (&__pyx_v_n_bonds), (&__pyx_v_from_atoms), (&__pyx_v_to_atoms)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
      |                                                                                                                              ^~
mdtraj/formats/tng/tng.c: In function '__pyx_pf_6mdtraj_7formats_3tng_17TNGTrajectoryFile_10_read_frame':
mdtraj/formats/tng/tng.c:6042:152: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare]
 6042 |     __pyx_t_1 = ((tng_util_pos_read_range(__pyx_v_self->_traj, __pyx_v_self->_pos, __pyx_v_self->_pos, (&__pyx_v_positions), (&__pyx_v_stride_length)) == __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
      |                                                                                                                                                        ^~
mdtraj/formats/tng/tng.c:6310:108: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare]
 6310 |   __pyx_t_1 = ((tng_util_time_of_frame_get(__pyx_v_self->_traj, __pyx_v_self->_pos, (&__pyx_v_frame_time)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
      |                                                                                                            ^~
mdtraj/formats/tng/tng.c:6412:304: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare]
 6412 |     __pyx_t_1 = ((tng_data_vector_interval_get(__pyx_v_self->_traj, __pyx_v_6mdtraj_7formats_3tng_TNG_TRAJ_BOX_SHAPE, __pyx_v_self->_pos, __pyx_v_self->_pos, __pyx_e_6mdtraj_7formats_3tng_TNG_USE_HASH, (&__pyx_v_box_shape), (&__pyx_v_stride_length), (&__pyx_v_n_values_per_frame), (&__pyx_v_data_type)) == __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
      |                                                                                                                                                                                                                                                                                                                ^~
mdtraj/formats/tng/tng.c: In function '__pyx_pf_6mdtraj_7formats_3tng_17TNGTrajectoryFile_16write':
mdtraj/formats/tng/tng.c:8904:94: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare]
 8904 |     __pyx_t_1 = ((tng_implicit_num_particles_set(__pyx_v_self->_traj, __pyx_v_self->n_atoms) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
      |                                                                                              ^~
mdtraj/formats/tng/tng.c:8936:75: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare]
 8936 |     __pyx_t_1 = ((tng_util_pos_write_interval_set(__pyx_v_self->_traj, 1) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
      |                                                                           ^~
mdtraj/formats/tng/tng.c:8968:81: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare]
 8968 |     __pyx_t_1 = ((tng_util_box_shape_write_interval_set(__pyx_v_self->_traj, 1) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
      |                                                                                 ^~
mdtraj/formats/tng/tng.c:9291:77: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare]
 9291 |       __pyx_t_9 = ((tng_time_per_frame_set(__pyx_v_self->_traj, __pyx_t_15) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
      |                                                                             ^~
mdtraj/formats/tng/tng.c:9482:372: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare]
 9482 |     __pyx_t_1 = ((tng_util_pos_write(__pyx_v_self->_traj, __pyx_v_self->tot_n_frames, (&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_xyz_array.rcbuffer->pybuffer.buf, __pyx_t_18, __pyx_pybuffernd_xyz_array.diminfo[0].strides, __pyx_t_19, __pyx_pybuffernd_xyz_array.diminfo[1].strides, __pyx_t_20, __pyx_pybuffernd_xyz_array.diminfo[2].strides)))) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
      |                                                                                                                                                                                                                                                                                                                                                                                    ^~
mdtraj/formats/tng/tng.c:9534:378: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare]
 9534 |     __pyx_t_1 = ((tng_util_box_shape_write(__pyx_v_self->_traj, __pyx_v_self->tot_n_frames, (&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_box_array.rcbuffer->pybuffer.buf, __pyx_t_20, __pyx_pybuffernd_box_array.diminfo[0].strides, __pyx_t_19, __pyx_pybuffernd_box_array.diminfo[1].strides, __pyx_t_18, __pyx_pybuffernd_box_array.diminfo[2].strides)))) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
      |                                                                                                                                                                                                                                                                                                                                                                                          ^~
mdtraj/formats/tng/tng.c:9596:89: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare]
 9596 |       __pyx_t_1 = ((tng_frame_set_first_frame_time_set(__pyx_v_self->_traj, __pyx_t_15) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
      |                                                                                         ^~
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_gen_data_block_add':
mdtraj/formats/tng/src/lib/tng_io.c:12613:9: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-truncation]
12613 |         strncpy(data->block_name, block_name, strlen(block_name) + 1);
      |         ^
mdtraj/formats/tng/src/lib/tng_io.c:12613:47: note: length computed here
12613 |         strncpy(data->block_name, block_name, strlen(block_name) + 1);
      |                                               ^~~~~~~~~~~~~~~~~~
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_data_block_write.isra':
mdtraj/formats/tng/src/lib/tng_io.c:5986:72: warning: 'num_first_particle' may be used uninitialized [-Wmaybe-uninitialized]
 5986 |                     for(j = num_first_particle; j < num_first_particle + n_particles;
      |                                                     ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
mdtraj/formats/tng/src/lib/tng_io.c:5684:26: note: 'num_first_particle' was declared here
 5684 |     int64_t n_particles, num_first_particle, n_frames, stride_length;
      |                          ^~~~~~~~~~~~~~~~~~
mdtraj/formats/tng/src/lib/tng_io.c:5986:72: warning: 'n_particles' may be used uninitialized [-Wmaybe-uninitialized]
 5986 |                     for(j = num_first_particle; j < num_first_particle + n_particles;
      |                                                     ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
mdtraj/formats/tng/src/lib/tng_io.c:5684:13: note: 'n_particles' was declared here
 5684 |     int64_t n_particles, num_first_particle, n_frames, stride_length;
      |             ^~~~~~~~~~~
INFO: aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-cpython-311/mdtraj/formats/tng/src/compression/bwlzh.o build/temp.linux-arm64-cpython-311/mdtraj/formats/tng/src/compression/bwt.o build/temp.linux-arm64-cpython-311/mdtraj/formats/tng/src/compression/coder.o build/temp.linux-arm64-cpython-311/mdtraj/formats/tng/src/compression/dict.o build/temp.linux-arm64-cpython-311/mdtraj/formats/tng/src/compression/fixpoint.o build/temp.linux-arm64-cpython-311/mdtraj/formats/tng/src/compression/huffman.o build/temp.linux-arm64-cpython-311/mdtraj/formats/tng/src/compression/huffmem.o build/temp.linux-arm64-cpython-311/mdtraj/formats/tng/src/compression/lz77.o build/temp.linux-arm64-cpython-311/mdtraj/formats/tng/src/compression/merge_sort.o build/temp.linux-arm64-cpython-311/mdtraj/formats/tng/src/compression/mtf.o build/temp.linux-arm64-cpython-311/mdtraj/formats/tng/src/compression/rle.o build/temp.linux-arm64-cpython-311/mdtraj/formats/tng/src/compression/tng_compress.o build/temp.linux-arm64-cpython-311/mdtraj/formats/tng/src/compression/vals16.o build/temp.linux-arm64-cpython-311/mdtraj/formats/tng/src/compression/warnmalloc.o build/temp.linux-arm64-cpython-311/mdtraj/formats/tng/src/compression/widemuldiv.o build/temp.linux-arm64-cpython-311/mdtraj/formats/tng/src/compression/xtc2.o build/temp.linux-arm64-cpython-311/mdtraj/formats/tng/src/compression/xtc3.o build/temp.linux-arm64-cpython-311/mdtraj/formats/tng/src/lib/md5.o build/temp.linux-arm64-cpython-311/mdtraj/formats/tng/src/lib/tng_io.o build/temp.linux-arm64-cpython-311/mdtraj/formats/tng/tng.o -L/usr/lib -L/usr/lib/aarch64-linux-gnu -lz -o /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/tng.cpython-311-aarch64-linux-gnu.so
building 'mdtraj.formats.dcd' extension
INFO: C compiler: aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC

INFO: compile options: '-Imdtraj/formats/dcd/include/ -Imdtraj/formats/dcd/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c'
extra options: '-Wno-unused-function -Wno-unreachable-code -Wno-sign-compare'
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/dcd/dcd.c
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/dcd/src/dcdplugin.c
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1940,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
                 from mdtraj/formats/dcd/dcd.c:776:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   17 | #warning "Using deprecated NumPy API, disable it with " \
      |  ^~~~~~~
mdtraj/formats/dcd/dcd.c: In function '__pyx_pf_6mdtraj_7formats_3dcd_17DCDTrajectoryFile_20read':
mdtraj/formats/dcd/dcd.c:688:40: warning: '__pyx_v_i' may be used uninitialized [-Wmaybe-uninitialized]
  688 |   #define PyInt_FromLong               PyLong_FromLong
      |                                        ^~~~~~~~~~~~~~~
mdtraj/formats/dcd/dcd.c:5434:7: note: '__pyx_v_i' was declared here
 5434 |   int __pyx_v_i;
      |       ^~~~~~~~~
INFO: aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-cpython-311/mdtraj/formats/dcd/dcd.o build/temp.linux-arm64-cpython-311/mdtraj/formats/dcd/src/dcdplugin.o -L/usr/lib/aarch64-linux-gnu -o /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/dcd.cpython-311-aarch64-linux-gnu.so
building 'mdtraj.formats.binpos' extension
INFO: C compiler: aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC

INFO: compile options: '-Imdtraj/formats/binpos/include/ -Imdtraj/formats/binpos/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c'
extra options: '-Wno-unused-function -Wno-unreachable-code -Wno-sign-compare'
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/binpos/binpos.c
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/binpos/src/binposplugin.c
mdtraj/formats/binpos/src/binposplugin.c: In function 'open_binpos_read':
mdtraj/formats/binpos/src/binposplugin.c:59:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
   59 |   fread(magicchar,sizeof(char),4,fd);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/binpos/src/binposplugin.c:69:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
   69 |   fread(&igarb,sizeof(int),1,fd);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1940,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
                 from mdtraj/formats/binpos/binpos.c:776:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   17 | #warning "Using deprecated NumPy API, disable it with " \
      |  ^~~~~~~
In function '__pyx_pf_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_8_read',
    inlined from '__pyx_pw_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_9_read' at mdtraj/formats/binpos/binpos.c:4980:13:
mdtraj/formats/binpos/binpos.c:5512:6: warning: '__pyx_v_status' may be used uninitialized [-Wmaybe-uninitialized]
 5512 |   if (__pyx_t_2) {
      |      ^
mdtraj/formats/binpos/binpos.c: In function '__pyx_pw_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_9_read':
mdtraj/formats/binpos/binpos.c:4992:7: note: '__pyx_v_status' was declared here
 4992 |   int __pyx_v_status;
      |       ^~~~~~~~~~~~~~
mdtraj/formats/binpos/binpos.c:688:40: warning: '__pyx_v_i' may be used uninitialized [-Wmaybe-uninitialized]
  688 |   #define PyInt_FromLong               PyLong_FromLong
      |                                        ^~~~~~~~~~~~~~~
mdtraj/formats/binpos/binpos.c:4989:7: note: '__pyx_v_i' was declared here
 4989 |   int __pyx_v_i;
      |       ^~~~~~~~~
INFO: aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-cpython-311/mdtraj/formats/binpos/binpos.o build/temp.linux-arm64-cpython-311/mdtraj/formats/binpos/src/binposplugin.o -L/usr/lib/aarch64-linux-gnu -o /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/binpos.cpython-311-aarch64-linux-gnu.so
building 'mdtraj.formats.dtr' extension
INFO: C compiler: aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC

INFO: compile options: '-DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c'
extra options: '-Wno-unused-function -Wno-unreachable-code -Wno-sign-compare'
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/dtr/dtr.cpp
INFO: aarch64-linux-gnu-gcc: mdtraj/formats/dtr/src/dtrplugin.cxx
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1940,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
                 from mdtraj/formats/dtr/dtr.cpp:797:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   17 | #warning "Using deprecated NumPy API, disable it with " \
      |  ^~~~~~~
mdtraj/formats/dtr/src/dtrplugin.cxx: In member function 'bool desres::molfile::Timekeys::init(const std::string&)':
mdtraj/formats/dtr/src/dtrplugin.cxx: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 constructor '{anonymous}::DDException::DDException(const std::string&, int)':
mdtraj/formats/dtr/src/dtrplugin.cxx:680:43: warning: '*this.{anonymous}::DDException::eno' is used uninitialized [-Wuninitialized]
  680 |       : std::runtime_error(text + strerror(eno)), eno(_eno){}
      |                                   ~~~~~~~~^~~~~
mdtraj/formats/dtr/src/dtrplugin.cxx: In function 'void DDmkdir(const std::string&, mode_t, int, int)':
mdtraj/formats/dtr/src/dtrplugin.cxx:706:23: warning: '%03x' directive writing between 3 and 8 bytes into a region of size 6 [-Wformat-overflow=]
  706 |         sprintf(sub, "%03x/", i);
      |                       ^~~~
mdtraj/formats/dtr/src/dtrplugin.cxx:706:22: note: directive argument in the range [0, 2147483646]
  706 |         sprintf(sub, "%03x/", i);
      |                      ^~~~~~~
In file included from /usr/include/stdio.h:906,
                 from mdtraj/formats/dtr/include/molfile_plugin.h:35,
                 from mdtraj/formats/dtr/include/dtrplugin.hxx:46,
                 from mdtraj/formats/dtr/src/dtrplugin.cxx:42:
In function 'int sprintf(char*, const char*, ...)',
    inlined from 'void DDmkdir(const std::string&, mode_t, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:706:9:
/usr/include/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 ());
      |                                   ~~~~~~~~~~~~~~~~~
INFO: aarch64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-cpython-311/mdtraj/formats/dtr/dtr.o build/temp.linux-arm64-cpython-311/mdtraj/formats/dtr/src/dtrplugin.o -L/usr/lib/aarch64-linux-gnu -o /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/dtr.cpython-311-aarch64-linux-gnu.so
building 'mdtraj._rmsd' extension
INFO: C compiler: aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC

INFO: compile options: '-Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c'
extra options: '-fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare'
INFO: aarch64-linux-gnu-gcc: mdtraj/rmsd/_rmsd.cpp
INFO: aarch64-linux-gnu-gcc: mdtraj/rmsd/src/center.cpp
INFO: aarch64-linux-gnu-gcc: mdtraj/rmsd/src/rotation.cpp
INFO: aarch64-linux-gnu-gcc: mdtraj/rmsd/src/theobald_rmsd.cpp
INFO: aarch64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-cpython-311/mdtraj/rmsd/_rmsd.o build/temp.linux-arm64-cpython-311/mdtraj/rmsd/src/center.o build/temp.linux-arm64-cpython-311/mdtraj/rmsd/src/rotation.o build/temp.linux-arm64-cpython-311/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/_rmsd.cpython-311-aarch64-linux-gnu.so
building 'mdtraj._lprmsd' extension
INFO: C compiler: aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC

INFO: compile options: '-Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c'
extra options: '-fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare'
INFO: aarch64-linux-gnu-gcc: mdtraj/rmsd/_lprmsd.cpp
INFO: aarch64-linux-gnu-gcc: mdtraj/rmsd/src/Munkres.cpp
INFO: aarch64-linux-gnu-gcc: mdtraj/rmsd/src/euclidean_permutation.cpp
INFO: aarch64-linux-gnu-gcc: mdtraj/rmsd/src/center.cpp
INFO: aarch64-linux-gnu-gcc: mdtraj/rmsd/src/fancy_index.cpp
INFO: aarch64-linux-gnu-gcc: mdtraj/rmsd/src/rotation.cpp
INFO: aarch64-linux-gnu-gcc: mdtraj/rmsd/src/theobald_rmsd.cpp
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1940,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
                 from mdtraj/rmsd/_lprmsd.cpp:806:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   17 | #warning "Using deprecated NumPy API, disable it with " \
      |  ^~~~~~~
INFO: aarch64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-cpython-311/mdtraj/rmsd/_lprmsd.o build/temp.linux-arm64-cpython-311/mdtraj/rmsd/src/Munkres.o build/temp.linux-arm64-cpython-311/mdtraj/rmsd/src/center.o build/temp.linux-arm64-cpython-311/mdtraj/rmsd/src/euclidean_permutation.o build/temp.linux-arm64-cpython-311/mdtraj/rmsd/src/fancy_index.o build/temp.linux-arm64-cpython-311/mdtraj/rmsd/src/rotation.o build/temp.linux-arm64-cpython-311/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/_lprmsd.cpython-311-aarch64-linux-gnu.so
building 'mdtraj.geometry._geometry' extension
INFO: C compiler: aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC

INFO: compile options: '-Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c'
extra options: '-fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare'
INFO: aarch64-linux-gnu-gcc: mdtraj/geometry/src/_geometry.cpp
INFO: aarch64-linux-gnu-gcc: mdtraj/geometry/src/dssp.cpp
INFO: aarch64-linux-gnu-gcc: mdtraj/geometry/src/sasa.cpp
INFO: aarch64-linux-gnu-gcc: mdtraj/geometry/src/geometry.cpp
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1940,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
                 from mdtraj/geometry/src/_geometry.cpp:808:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   17 | #warning "Using deprecated NumPy API, disable it with " \
      |  ^~~~~~~
mdtraj/geometry/src/_geometry.cpp: In function 'void __pyx_f_6mdtraj_8geometry_9_geometry_make_whole(__Pyx_memviewslice, __Pyx_memviewslice, __Pyx_memviewslice)':
mdtraj/geometry/src/_geometry.cpp:6084:224: warning: '__pyx_v_delta[2]' may be used uninitialized [-Wmaybe-uninitialized]
 6084 |       (__pyx_v_offset[__pyx_v_k]) = ((*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_frame_unitcell_vectors.data + __pyx_t_8 * __pyx_v_frame_unitcell_vectors.strides[0]) )) + __pyx_t_7)) ))) * roundf(((__pyx_v_delta[2]) / (*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_frame_unitcell_vectors.data + __pyx_t_5 * __pyx_v_frame_unitcell_vectors.strides[0]) )) + __pyx_t_4)) ))))));
      |                                                                                                                                                                                                                          ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/geometry/src/_geometry.cpp:6005:9: note: '__pyx_v_delta[2]' was declared here
 6005 |   float __pyx_v_delta[3];
      |         ^~~~~~~~~~~~~
mdtraj/geometry/src/_geometry.cpp:6098:277: warning: '__pyx_v_delta[1]' may be used uninitialized [-Wmaybe-uninitialized]
 6098 |       (__pyx_v_offset[__pyx_t_9]) = ((__pyx_v_offset[__pyx_t_9]) + ((*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_frame_unitcell_vectors.data + __pyx_t_4 * __pyx_v_frame_unitcell_vectors.strides[0]) )) + __pyx_t_5)) ))) * roundf((((__pyx_v_delta[1]) - (__pyx_v_offset[1])) / (*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_frame_unitcell_vectors.data + __pyx_t_7 * __pyx_v_frame_unitcell_vectors.strides[0]) )) + __pyx_t_8)) )))))));
      |                                                                                                                                                                                                                                                                 ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
mdtraj/geometry/src/_geometry.cpp:6005:9: note: '__pyx_v_delta[1]' was declared here
 6005 |   float __pyx_v_delta[3];
      |         ^~~~~~~~~~~~~
mdtraj/geometry/src/_geometry.cpp:6098:277: warning: '__pyx_v_offset[1]' may be used uninitialized [-Wmaybe-uninitialized]
 6098 |       (__pyx_v_offset[__pyx_t_9]) = ((__pyx_v_offset[__pyx_t_9]) + ((*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_frame_unitcell_vectors.data + __pyx_t_4 * __pyx_v_frame_unitcell_vectors.strides[0]) )) + __pyx_t_5)) ))) * roundf((((__pyx_v_delta[1]) - (__pyx_v_offset[1])) / (*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_frame_unitcell_vectors.data + __pyx_t_7 * __pyx_v_frame_unitcell_vectors.strides[0]) )) + __pyx_t_8)) )))))));
      |                                                                                                                                                                                                                                                                 ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
mdtraj/geometry/src/_geometry.cpp:6004:9: note: '__pyx_v_offset[1]' was declared here
 6004 |   float __pyx_v_offset[3];
      |         ^~~~~~~~~~~~~~
INFO: aarch64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-cpython-311/mdtraj/geometry/src/_geometry.o build/temp.linux-arm64-cpython-311/mdtraj/geometry/src/dssp.o build/temp.linux-arm64-cpython-311/mdtraj/geometry/src/geometry.o build/temp.linux-arm64-cpython-311/mdtraj/geometry/src/sasa.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/_geometry.cpython-311-aarch64-linux-gnu.so
building 'mdtraj.geometry.drid' extension
INFO: C compiler: aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC

INFO: compile options: '-Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c'
extra options: '-fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare'
INFO: aarch64-linux-gnu-gcc: mdtraj/geometry/drid.cpp
INFO: aarch64-linux-gnu-gcc: mdtraj/geometry/src/dridkernels.cpp
INFO: aarch64-linux-gnu-gcc: mdtraj/geometry/src/moments.cpp
INFO: aarch64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-cpython-311/mdtraj/geometry/drid.o build/temp.linux-arm64-cpython-311/mdtraj/geometry/src/dridkernels.o build/temp.linux-arm64-cpython-311/mdtraj/geometry/src/moments.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/drid.cpython-311-aarch64-linux-gnu.so
building 'mdtraj.geometry.neighbors' extension
INFO: C compiler: aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC

INFO: compile options: '-Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c'
extra options: '-fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare'
INFO: aarch64-linux-gnu-gcc: mdtraj/geometry/neighbors.cpp
INFO: aarch64-linux-gnu-gcc: mdtraj/geometry/src/neighbors.cpp
INFO: aarch64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-cpython-311/mdtraj/geometry/neighbors.o build/temp.linux-arm64-cpython-311/mdtraj/geometry/src/neighbors.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/neighbors.cpython-311-aarch64-linux-gnu.so
building 'mdtraj.geometry.neighborlist' extension
INFO: C compiler: aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC

INFO: compile options: '-Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c'
extra options: '-fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare'
INFO: aarch64-linux-gnu-gcc: mdtraj/geometry/neighborlist.cpp
INFO: aarch64-linux-gnu-gcc: mdtraj/geometry/src/neighborlist.cpp
In constructor 'Voxels::Voxels(float, float, float, float, float, float, const float (&)[3][3], bool)',
    inlined from 'std::vector<std::vector<int> > _compute_neighborlist(const float*, int, float, const float*)' at mdtraj/geometry/src/neighborlist.cpp:377:116:
mdtraj/geometry/src/neighborlist.cpp:50:53: warning: 'periodicBoxVectors' may be used uninitialized [-Wmaybe-uninitialized]
   50 |         periodicBoxSize[0] = periodicBoxVectors[0][0];
      |                              ~~~~~~~~~~~~~~~~~~~~~~~^
mdtraj/geometry/src/neighborlist.cpp: In function 'std::vector<std::vector<int> > _compute_neighborlist(const float*, int, float, const float*)':
mdtraj/geometry/src/neighborlist.cpp:341:11: note: 'periodicBoxVectors' declared here
  341 |     float periodicBoxVectors[3][3];
      |           ^~~~~~~~~~~~~~~~~~
In constructor 'Voxels::Voxels(float, float, float, float, float, float, const float (&)[3][3], bool)',
    inlined from 'std::vector<std::vector<int> > _compute_neighborlist(const float*, int, float, const float*)' at mdtraj/geometry/src/neighborlist.cpp:377:116:
mdtraj/geometry/src/neighborlist.cpp:51:53: warning: 'periodicBoxVectors' may be used uninitialized [-Wmaybe-uninitialized]
   51 |         periodicBoxSize[1] = periodicBoxVectors[1][1];
      |                              ~~~~~~~~~~~~~~~~~~~~~~~^
mdtraj/geometry/src/neighborlist.cpp: In function 'std::vector<std::vector<int> > _compute_neighborlist(const float*, int, float, const float*)':
mdtraj/geometry/src/neighborlist.cpp:341:11: note: 'periodicBoxVectors' declared here
  341 |     float periodicBoxVectors[3][3];
      |           ^~~~~~~~~~~~~~~~~~
In constructor 'Voxels::Voxels(float, float, float, float, float, float, const float (&)[3][3], bool)',
    inlined from 'std::vector<std::vector<int> > _compute_neighborlist(const float*, int, float, const float*)' at mdtraj/geometry/src/neighborlist.cpp:377:116:
mdtraj/geometry/src/neighborlist.cpp:52:53: warning: 'periodicBoxVectors' may be used uninitialized [-Wmaybe-uninitialized]
   52 |         periodicBoxSize[2] = periodicBoxVectors[2][2];
      |                              ~~~~~~~~~~~~~~~~~~~~~~~^
mdtraj/geometry/src/neighborlist.cpp: In function 'std::vector<std::vector<int> > _compute_neighborlist(const float*, int, float, const float*)':
mdtraj/geometry/src/neighborlist.cpp:341:11: note: 'periodicBoxVectors' declared here
  341 |     float periodicBoxVectors[3][3];
      |           ^~~~~~~~~~~~~~~~~~
In constructor 'Voxels::Voxels(float, float, float, float, float, float, const float (&)[3][3], bool)',
    inlined from 'std::vector<std::vector<int> > _compute_neighborlist(const float*, int, float, const float*)' at mdtraj/geometry/src/neighborlist.cpp:377:116:
mdtraj/geometry/src/neighborlist.cpp:56:45: warning: 'periodicBoxVectors' may be used uninitialized [-Wmaybe-uninitialized]
   56 |         triclinic = (periodicBoxVectors[0][1] != 0.0 || periodicBoxVectors[0][2] != 0.0 ||
      |                      ~~~~~~~~~~~~~~~~~~~~~~~^
mdtraj/geometry/src/neighborlist.cpp: In function 'std::vector<std::vector<int> > _compute_neighborlist(const float*, int, float, const float*)':
mdtraj/geometry/src/neighborlist.cpp:341:11: note: 'periodicBoxVectors' declared here
  341 |     float periodicBoxVectors[3][3];
      |           ^~~~~~~~~~~~~~~~~~
INFO: aarch64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-cpython-311/mdtraj/geometry/neighborlist.o build/temp.linux-arm64-cpython-311/mdtraj/geometry/src/neighborlist.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/neighborlist.cpython-311-aarch64-linux-gnu.so
running install_lib
creating /build/mdtraj-1.9.7/debian/python3-mdtraj
creating /build/mdtraj-1.9.7/debian/python3-mdtraj/usr
creating /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib
creating /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11
creating /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages
creating /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/_lprmsd.cpython-311-aarch64-linux-gnu.so -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/_rmsd.cpython-311-aarch64-linux-gnu.so -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/version.py -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj
creating /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/__pycache__
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/__pycache__/version.cpython-311.pyc -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/__pycache__
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/__pycache__/__init__.cpython-311.pyc -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/__pycache__
creating /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core
creating /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core/__pycache__
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core/__pycache__/trajectory.cpython-311.pyc -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core/__pycache__
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core/__pycache__/selection.cpython-311.pyc -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core/__pycache__
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core/__pycache__/residue_names.cpython-311.pyc -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core/__pycache__
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core/__pycache__/topology.cpython-311.pyc -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core/__pycache__
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core/__pycache__/element.cpython-311.pyc -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core/__pycache__
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core/__pycache__/__init__.cpython-311.pyc -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core/__pycache__
creating /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core/lib
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core/lib/center.h -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core/lib
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core/lib/theobald_rmsd.h -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core/lib
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core/lib/libtheobald.a -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core/lib
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core/__init__.py -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core/element.py -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core/residue_names.py -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core/selection.py -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core/topology.py -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core/trajectory.py -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core
creating /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/dtr.cpython-311-aarch64-linux-gnu.so -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/binpos.cpython-311-aarch64-linux-gnu.so -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/dcd.cpython-311-aarch64-linux-gnu.so -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/tng.cpython-311-aarch64-linux-gnu.so -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/trr.cpython-311-aarch64-linux-gnu.so -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/xtc.cpython-311-aarch64-linux-gnu.so -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats
creating /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/__pycache__
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/__pycache__/gsd.cpython-311.pyc -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/__pycache__
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/__pycache__/hoomdxml.cpython-311.pyc -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/__pycache__
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/__pycache__/mol2.cpython-311.pyc -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/__pycache__
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/__pycache__/psf.cpython-311.pyc -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/__pycache__
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/__pycache__/prmtop.cpython-311.pyc -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/__pycache__
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/__pycache__/openmmxml.cpython-311.pyc -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/__pycache__
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/__pycache__/xyzfile.cpython-311.pyc -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/__pycache__
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/__pycache__/gro.cpython-311.pyc -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/__pycache__
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/__pycache__/lammpstrj.cpython-311.pyc -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/__pycache__
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/__pycache__/amberrst.cpython-311.pyc -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/__pycache__
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/__pycache__/mdcrd.cpython-311.pyc -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/__pycache__
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/__pycache__/lh5.cpython-311.pyc -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/__pycache__
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/__pycache__/netcdf.cpython-311.pyc -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/__pycache__
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/__pycache__/hdf5.cpython-311.pyc -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/__pycache__
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/__pycache__/registry.cpython-311.pyc -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/__pycache__
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/__pycache__/arc.cpython-311.pyc -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/__pycache__
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/__pycache__/__init__.cpython-311.pyc -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/__pycache__
creating /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/pdb
creating /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/pdb/__pycache__
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/pdb/__pycache__/pdbstructure.cpython-311.pyc -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/pdb/__pycache__
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/pdb/__pycache__/pdbfile.cpython-311.pyc -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/pdb/__pycache__
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/pdb/__pycache__/__init__.cpython-311.pyc -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/pdb/__pycache__
creating /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/pdb/data
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/pdb/data/pdbNames.xml -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/pdb/data
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/pdb/data/residues.xml -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/pdb/data
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/pdb/__init__.py -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/pdb
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/pdb/pdbfile.py -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/pdb
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/pdb/pdbstructure.py -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/pdb
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/__init__.py -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/amberrst.py -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/arc.py -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/gro.py -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/gsd.py -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/hdf5.py -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/hoomdxml.py -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/lammpstrj.py -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/lh5.py -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/mdcrd.py -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/mol2.py -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/netcdf.py -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/openmmxml.py -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/prmtop.py -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/psf.py -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/registry.py -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/xyzfile.py -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats
creating /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/neighborlist.cpython-311-aarch64-linux-gnu.so -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/neighbors.cpython-311-aarch64-linux-gnu.so -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/drid.cpython-311-aarch64-linux-gnu.so -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/_geometry.cpython-311-aarch64-linux-gnu.so -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry
creating /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/__pycache__
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/__pycache__/shape.cpython-311.pyc -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/__pycache__
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/__pycache__/order.cpython-311.pyc -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/__pycache__
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/__pycache__/rdf.cpython-311.pyc -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/__pycache__
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/__pycache__/thermodynamic_properties.cpython-311.pyc -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/__pycache__
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/__pycache__/dssp.cpython-311.pyc -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/__pycache__
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/__pycache__/contact.cpython-311.pyc -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/__pycache__
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/__pycache__/sasa.cpython-311.pyc -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/__pycache__
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/__pycache__/hbond.cpython-311.pyc -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/__pycache__
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/__pycache__/dihedral.cpython-311.pyc -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/__pycache__
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/__pycache__/distance.cpython-311.pyc -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/__pycache__
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/__pycache__/angle.cpython-311.pyc -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/__pycache__
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/__pycache__/rg.cpython-311.pyc -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/__pycache__
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/__pycache__/__init__.cpython-311.pyc -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/__pycache__
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/__init__.py -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/alignment.py -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/angle.py -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/contact.py -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/dihedral.py -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/distance.py -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/dssp.py -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/hbond.py -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/internal.py -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/order.py -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/rdf.py -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/rg.py -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/sasa.py -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/shape.py -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/thermodynamic_properties.py -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry
creating /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/nmr
creating /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/nmr/__pycache__
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/nmr/__pycache__/scalar_couplings.cpython-311.pyc -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/nmr/__pycache__
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/nmr/__pycache__/shift_wrappers.cpython-311.pyc -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/nmr/__pycache__
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/nmr/__pycache__/__init__.cpython-311.pyc -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/nmr/__pycache__
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/nmr/__init__.py -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/nmr
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/nmr/scalar_couplings.py -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/nmr
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/nmr/shift_wrappers.py -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/nmr
creating /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/reporters
creating /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/reporters/__pycache__
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/reporters/__pycache__/xtcreporter.cpython-311.pyc -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/reporters/__pycache__
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/reporters/__pycache__/dcdreporter.cpython-311.pyc -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/reporters/__pycache__
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/reporters/__pycache__/netcdfreporter.cpython-311.pyc -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/reporters/__pycache__
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/reporters/__pycache__/basereporter.cpython-311.pyc -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/reporters/__pycache__
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/reporters/__pycache__/hdf5reporter.cpython-311.pyc -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/reporters/__pycache__
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/reporters/__pycache__/__init__.cpython-311.pyc -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/reporters/__pycache__
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/reporters/__init__.py -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/reporters
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/reporters/basereporter.py -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/reporters
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/reporters/dcdreporter.py -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/reporters
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/reporters/hdf5reporter.py -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/reporters
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/reporters/netcdfreporter.py -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/reporters
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/reporters/xtcreporter.py -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/reporters
creating /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/scripts
creating /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/scripts/__pycache__
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/scripts/__pycache__/__init__.cpython-311.pyc -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/scripts/__pycache__
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/scripts/__init__.py -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/scripts
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/scripts/mdconvert.py -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/scripts
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/scripts/mdinspect.py -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/scripts
creating /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/testing
creating /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/testing/__pycache__
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/testing/__pycache__/docscrape.cpython-311.pyc -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/testing/__pycache__
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/testing/__pycache__/docstrings.cpython-311.pyc -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/testing/__pycache__
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/testing/__pycache__/testing.cpython-311.pyc -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/testing/__pycache__
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/testing/__pycache__/__init__.cpython-311.pyc -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/testing/__pycache__
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/testing/__init__.py -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/testing
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/testing/docscrape.py -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/testing
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/testing/docstrings.py -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/testing
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/testing/testing.py -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/testing
creating /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils
creating /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/__pycache__
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/__pycache__/singleton.cpython-311.pyc -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/__pycache__
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/__pycache__/zipped.cpython-311.pyc -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/__pycache__
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/__pycache__/contextmanagers.cpython-311.pyc -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/__pycache__
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/__pycache__/unitcell.cpython-311.pyc -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/__pycache__
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/__pycache__/rotation.cpython-311.pyc -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/__pycache__
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/__pycache__/six.cpython-311.pyc -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/__pycache__
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/__pycache__/validation.cpython-311.pyc -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/__pycache__
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/__pycache__/delay_import.cpython-311.pyc -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/__pycache__
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/__pycache__/__init__.cpython-311.pyc -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/__pycache__
creating /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit
creating /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit/__pycache__
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/__pycache__/prefix.cpython-311.pyc -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit/__pycache__
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/__pycache__/unit_operators.cpython-311.pyc -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit/__pycache__
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/__pycache__/unit_definitions.cpython-311.pyc -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit/__pycache__
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/__pycache__/baseunit.cpython-311.pyc -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit/__pycache__
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/__pycache__/mymatrix.cpython-311.pyc -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit/__pycache__
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/__pycache__/unit.cpython-311.pyc -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit/__pycache__
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/__pycache__/basedimension.cpython-311.pyc -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit/__pycache__
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/__pycache__/standard_dimensions.cpython-311.pyc -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit/__pycache__
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/__pycache__/quantity.cpython-311.pyc -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit/__pycache__
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/__pycache__/__init__.cpython-311.pyc -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit/__pycache__
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/__init__.py -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/basedimension.py -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/baseunit.py -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/doctests.py -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/mymatrix.py -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/unit.py -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/constants.py -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/prefix.py -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/quantity.py -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/standard_dimensions.py -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/unit_definitions.py -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/unit_math.py -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/unit_operators.py -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/__init__.py -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/contextmanagers.py -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/delay_import.py -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/rotation.py -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/singleton.py -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/six.py -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unitcell.py -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/validation.py -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/zipped.py -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/__init__.py -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj
copying /build/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/io.py -> /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj
byte-compiling /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/version.py to version.cpython-311.pyc
byte-compiling /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core/__init__.py to __init__.cpython-311.pyc
byte-compiling /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core/element.py to element.cpython-311.pyc
byte-compiling /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core/residue_names.py to residue_names.cpython-311.pyc
byte-compiling /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core/selection.py to selection.cpython-311.pyc
byte-compiling /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core/topology.py to topology.cpython-311.pyc
byte-compiling /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core/trajectory.py to trajectory.cpython-311.pyc
byte-compiling /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/pdb/__init__.py to __init__.cpython-311.pyc
byte-compiling /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/pdb/pdbfile.py to pdbfile.cpython-311.pyc
byte-compiling /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/pdb/pdbstructure.py to pdbstructure.cpython-311.pyc
byte-compiling /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/__init__.py to __init__.cpython-311.pyc
byte-compiling /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/amberrst.py to amberrst.cpython-311.pyc
byte-compiling /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/arc.py to arc.cpython-311.pyc
byte-compiling /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/gro.py to gro.cpython-311.pyc
byte-compiling /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/gsd.py to gsd.cpython-311.pyc
byte-compiling /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/hdf5.py to hdf5.cpython-311.pyc
byte-compiling /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/hoomdxml.py to hoomdxml.cpython-311.pyc
byte-compiling /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/lammpstrj.py to lammpstrj.cpython-311.pyc
byte-compiling /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/lh5.py to lh5.cpython-311.pyc
byte-compiling /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/mdcrd.py to mdcrd.cpython-311.pyc
byte-compiling /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/mol2.py to mol2.cpython-311.pyc
byte-compiling /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/netcdf.py to netcdf.cpython-311.pyc
byte-compiling /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/openmmxml.py to openmmxml.cpython-311.pyc
byte-compiling /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/prmtop.py to prmtop.cpython-311.pyc
byte-compiling /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/psf.py to psf.cpython-311.pyc
byte-compiling /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/registry.py to registry.cpython-311.pyc
byte-compiling /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/xyzfile.py to xyzfile.cpython-311.pyc
byte-compiling /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/__init__.py to __init__.cpython-311.pyc
byte-compiling /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/alignment.py to alignment.cpython-311.pyc
byte-compiling /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/angle.py to angle.cpython-311.pyc
byte-compiling /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/contact.py to contact.cpython-311.pyc
byte-compiling /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/dihedral.py to dihedral.cpython-311.pyc
byte-compiling /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/distance.py to distance.cpython-311.pyc
byte-compiling /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/dssp.py to dssp.cpython-311.pyc
byte-compiling /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/hbond.py to hbond.cpython-311.pyc
byte-compiling /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/internal.py to internal.cpython-311.pyc
byte-compiling /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/order.py to order.cpython-311.pyc
byte-compiling /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/rdf.py to rdf.cpython-311.pyc
byte-compiling /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/rg.py to rg.cpython-311.pyc
byte-compiling /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/sasa.py to sasa.cpython-311.pyc
byte-compiling /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/shape.py to shape.cpython-311.pyc
byte-compiling /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/thermodynamic_properties.py to thermodynamic_properties.cpython-311.pyc
byte-compiling /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/nmr/__init__.py to __init__.cpython-311.pyc
byte-compiling /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/nmr/scalar_couplings.py to scalar_couplings.cpython-311.pyc
byte-compiling /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/nmr/shift_wrappers.py to shift_wrappers.cpython-311.pyc
byte-compiling /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/reporters/__init__.py to __init__.cpython-311.pyc
byte-compiling /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/reporters/basereporter.py to basereporter.cpython-311.pyc
byte-compiling /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/reporters/dcdreporter.py to dcdreporter.cpython-311.pyc
byte-compiling /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/reporters/hdf5reporter.py to hdf5reporter.cpython-311.pyc
byte-compiling /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/reporters/netcdfreporter.py to netcdfreporter.cpython-311.pyc
byte-compiling /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/reporters/xtcreporter.py to xtcreporter.cpython-311.pyc
byte-compiling /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/scripts/__init__.py to __init__.cpython-311.pyc
byte-compiling /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/scripts/mdconvert.py to mdconvert.cpython-311.pyc
byte-compiling /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/scripts/mdinspect.py to mdinspect.cpython-311.pyc
byte-compiling /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/testing/__init__.py to __init__.cpython-311.pyc
byte-compiling /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/testing/docscrape.py to docscrape.cpython-311.pyc
byte-compiling /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/testing/docstrings.py to docstrings.cpython-311.pyc
byte-compiling /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/testing/testing.py to testing.cpython-311.pyc
byte-compiling /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit/__init__.py to __init__.cpython-311.pyc
byte-compiling /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit/basedimension.py to basedimension.cpython-311.pyc
byte-compiling /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit/baseunit.py to baseunit.cpython-311.pyc
byte-compiling /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit/doctests.py to doctests.cpython-311.pyc
byte-compiling /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit/mymatrix.py to mymatrix.cpython-311.pyc
byte-compiling /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit/unit.py to unit.cpython-311.pyc
byte-compiling /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit/constants.py to constants.cpython-311.pyc
byte-compiling /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit/prefix.py to prefix.cpython-311.pyc
byte-compiling /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit/quantity.py to quantity.cpython-311.pyc
byte-compiling /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit/standard_dimensions.py to standard_dimensions.cpython-311.pyc
byte-compiling /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit/unit_definitions.py to unit_definitions.cpython-311.pyc
byte-compiling /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit/unit_math.py to unit_math.cpython-311.pyc
byte-compiling /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit/unit_operators.py to unit_operators.cpython-311.pyc
byte-compiling /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/__init__.py to __init__.cpython-311.pyc
byte-compiling /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/contextmanagers.py to contextmanagers.cpython-311.pyc
byte-compiling /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/delay_import.py to delay_import.cpython-311.pyc
byte-compiling /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/rotation.py to rotation.cpython-311.pyc
byte-compiling /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/singleton.py to singleton.cpython-311.pyc
byte-compiling /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/six.py to six.cpython-311.pyc
byte-compiling /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unitcell.py to unitcell.cpython-311.pyc
byte-compiling /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/validation.py to validation.cpython-311.pyc
byte-compiling /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/zipped.py to zipped.cpython-311.pyc
byte-compiling /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/__init__.py to __init__.cpython-311.pyc
byte-compiling /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/io.py to io.cpython-311.pyc
running install_egg_info
running egg_info
creating mdtraj.egg-info
writing mdtraj.egg-info/PKG-INFO
writing dependency_links to mdtraj.egg-info/dependency_links.txt
writing entry points to mdtraj.egg-info/entry_points.txt
writing requirements to mdtraj.egg-info/requires.txt
writing top-level names to mdtraj.egg-info/top_level.txt
writing manifest file 'mdtraj.egg-info/SOURCES.txt'
reading manifest file 'mdtraj.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
no previously-included directories found matching '__pycache__'
no previously-included directories found matching '*.pyc'
adding license file 'LICENSE'
writing manifest file 'mdtraj.egg-info/SOURCES.txt'
Copying mdtraj.egg-info to /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj-1.9.7.egg-info
Skipping SOURCES.txt
running install_scripts
Installing mdconvert-mdtraj script to /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/bin
Installing mdinspect script to /build/mdtraj-1.9.7/debian/python3-mdtraj/usr/bin
   debian/rules override_dh_install
make[1]: Entering directory '/build/mdtraj-1.9.7'
dh_install
dh_numpy3
make[1]: Leaving directory '/build/mdtraj-1.9.7'
   dh_installdocs -O--buildsystem=pybuild
dh_installdocs: warning: Cannot auto-detect main package for python-mdtraj-doc.  If the default is wrong, please use --doc-main-package
   debian/rules override_dh_sphinxdoc-indep
make[1]: Entering directory '/build/mdtraj-1.9.7'
dh_sphinxdoc -i
dh_sphinxdoc: warning: ignoring unknown JavaScript code: debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/js/versions.js
sed "s|src=\"https://img.shields.io/badge/DOI-10.1016%2Fj.bpj.2015.08.015-blue.svg\"|src=\"_static/doi-10.1016_j.bpj.2015.08.015-blue.svg\"|g" -i debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/index.html
make[1]: Leaving directory '/build/mdtraj-1.9.7'
   dh_sphinxdoc -O--buildsystem=pybuild -Npython-mdtraj-doc
dh_sphinxdoc: warning: Sphinx documentation not found
   dh_installchangelogs -O--buildsystem=pybuild
   dh_installexamples -O--buildsystem=pybuild
dh_installexamples: warning: Cannot auto-detect main package for python-mdtraj-doc.  If the default is wrong, please use --doc-main-package
   dh_installman -O--buildsystem=pybuild
   dh_python3 -O--buildsystem=pybuild
   dh_installsystemduser -O--buildsystem=pybuild
   dh_perl -O--buildsystem=pybuild
   dh_link -O--buildsystem=pybuild
   dh_strip_nondeterminism -O--buildsystem=pybuild
   dh_compress -O--buildsystem=pybuild
   dh_fixperms -O--buildsystem=pybuild
   dh_missing -O--buildsystem=pybuild
   dh_dwz -a -O--buildsystem=pybuild
   dh_strip -a -O--buildsystem=pybuild
   dh_makeshlibs -a -O--buildsystem=pybuild
   dh_shlibdeps -a -O--buildsystem=pybuild
   dh_installdeb -O--buildsystem=pybuild
   dh_gencontrol -O--buildsystem=pybuild
dpkg-gencontrol: warning: package python-mdtraj-doc: substitution variable ${python3:Depends} unused, but is defined
dpkg-gencontrol: warning: package python-mdtraj-doc: substitution variable ${sphinxdoc:Built-Using} unused, but is defined
   dh_md5sums -O--buildsystem=pybuild
   dh_builddeb -O--buildsystem=pybuild
dpkg-deb: building package 'python3-mdtraj-dbgsym' in '../python3-mdtraj-dbgsym_1.9.7-6_arm64.deb'.
dpkg-deb: building package 'python3-mdtraj' in '../python3-mdtraj_1.9.7-6_arm64.deb'.
dpkg-deb: building package 'python-mdtraj-doc' in '../python-mdtraj-doc_1.9.7-6_all.deb'.
 dpkg-genbuildinfo --build=binary -O../mdtraj_1.9.7-6_arm64.buildinfo
 dpkg-genchanges --build=binary -O../mdtraj_1.9.7-6_arm64.changes
dpkg-genchanges: info: binary-only upload (no source code included)
 dpkg-source --after-build .
dpkg-source: info: using options from mdtraj-1.9.7/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/
dpkg-buildpackage: info: binary-only upload (no source included)
dpkg-genchanges: info: not including original source code in upload
I: copying local configuration
I: 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/20111 and its subdirectories
I: Current time: Fri Apr 14 22:47:18 -12 2023
I: pbuilder-time-stamp: 1681555638
Sat Apr 15 10:48:11 UTC 2023  I: 1st build successful. Starting 2nd build on remote node codethink9-arm64.debian.net.
Sat Apr 15 10:48:11 UTC 2023  I: Preparing to do remote build '2' on codethink9-arm64.debian.net.
Sat Apr 15 11:11:50 UTC 2023  I: Deleting $TMPDIR on codethink9-arm64.debian.net.
Sat Apr 15 11:11:51 UTC 2023  I: mdtraj_1.9.7-6_arm64.changes:
Format: 1.8
Date: Wed, 01 Mar 2023 11:54:43 +0100
Source: mdtraj
Binary: python-mdtraj-doc python3-mdtraj python3-mdtraj-dbgsym
Architecture: all arm64
Version: 1.9.7-6
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 (1.9.7-6) unstable; urgency=medium
 .
   * update debian patch test_relax_tol.patch to relax tolerance in
     periodic test in test_distances_t (test_distance.py).
     Was occasionally failing on arm64.
Checksums-Sha1:
 9481478169669e6cca1c35f2abde30aa3db00582 12992 mdtraj_1.9.7-6_arm64.buildinfo
 7a1792dbad706bc03c6dad2bb5e7d7972e4a426c 698540 python-mdtraj-doc_1.9.7-6_all.deb
 0dcad3c8f49b192b1c5cd6c7cedcdc63fc659420 5403644 python3-mdtraj-dbgsym_1.9.7-6_arm64.deb
 c6b81544197c19f108f0b402f25913c3207a538c 963788 python3-mdtraj_1.9.7-6_arm64.deb
Checksums-Sha256:
 4804ac2b33ffee45cc817a17d4e194db7c77bd40e5ebe3d11a35564d619c3cf4 12992 mdtraj_1.9.7-6_arm64.buildinfo
 823f57a30be3587a1b62bc9c2d1c21cfba30e096c0aed4cf3d32eb70d13402ab 698540 python-mdtraj-doc_1.9.7-6_all.deb
 af17a4f4a21394579bae5b0c8a18ac101833e2c23cd7ba030d5885543cb49947 5403644 python3-mdtraj-dbgsym_1.9.7-6_arm64.deb
 d81f6b47fe54089b578464d037a48c1c619a658c273c775e6682003183cf056f 963788 python3-mdtraj_1.9.7-6_arm64.deb
Files:
 e613c3a89b653b89d5f2825db9be5e81 12992 python optional mdtraj_1.9.7-6_arm64.buildinfo
 0fd0bd72b987e450404e3a488a3b785e 698540 doc optional python-mdtraj-doc_1.9.7-6_all.deb
 1d03c97a500e281fc75204f2a1b80f9e 5403644 debug optional python3-mdtraj-dbgsym_1.9.7-6_arm64.deb
 1ee2feac5ad0d80346e4399446415cb9 963788 python optional python3-mdtraj_1.9.7-6_arm64.deb
Sat Apr 15 11:11:52 UTC 2023  I: diffoscope 240 will be used to compare the two builds:
# Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.qrvXaQUi/mdtraj_1.9.7-6.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.qrvXaQUi/mdtraj_1.9.7-6.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.qrvXaQUi/mdtraj_1.9.7-6.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.qrvXaQUi/b1/mdtraj_1.9.7-6_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.qrvXaQUi/b2/mdtraj_1.9.7-6_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     abc.DotChangesFile

## main (total time: 0.447s)
       0.447s      2 calls    outputs
       0.000s      1 call     cleanup

## recognizes (total time: 0.101s)
       0.101s     12 calls    diffoscope.comparators.binary.FilesystemFile
       0.000s     10 calls    abc.DotChangesFile

## specialize (total time: 0.000s)
       0.000s      1 call     specialize
Sat Apr 15 11:11:54 UTC 2023  I: diffoscope 240 found no differences in the changes files, and a .buildinfo file also exists.
Sat Apr 15 11:11:54 UTC 2023  I: mdtraj from bookworm built successfully and reproducibly on arm64.
Sat Apr 15 11:11:55 UTC 2023  I: Submitting .buildinfo files to external archives:
Sat Apr 15 11:11:55 UTC 2023  I: Submitting 16K	b1/mdtraj_1.9.7-6_arm64.buildinfo.asc
Sat Apr 15 11:11:57 UTC 2023  I: Submitting 16K	b2/mdtraj_1.9.7-6_arm64.buildinfo.asc
Sat Apr 15 11:11:57 UTC 2023  I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit.
Sat Apr 15 11:11:57 UTC 2023  I: Done submitting .buildinfo files.
Sat Apr 15 11:11:57 UTC 2023  I: Removing signed mdtraj_1.9.7-6_arm64.buildinfo.asc files:
removed './b1/mdtraj_1.9.7-6_arm64.buildinfo.asc'
removed './b2/mdtraj_1.9.7-6_arm64.buildinfo.asc'