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 -----BEGIN PGP SIGNED MESSAGE----- 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 Uploaders: Drew Parsons 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 -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEI8mpPlhYGekSbQo2Vz7x5L1aAfoFAmP/Lz8UHGRwYXJzb25z QGRlYmlhbi5vcmcACgkQVz7x5L1aAfpfdA/+IsZkcZRELp4j3ljessKZP9zSHGc+ utPdG9wIimtjnUo+m+hyKh3PYchar17/i9VcVYd10BB77VHXpjVcrbffDWmyOQi6 Y4auUdooPTalsGk70eBCeLq6s9nQg6QEFVIwJvx1gDulCridNDIz87Tf1HCAVx3t /yZAmYWWy5Q0yNDB7h/Xc3ESPM7tqK+BYuNDboI7O2ATV8X0BKfcJAsCaYHc1xwn 9GsgHLxoPN8WeGe2IHwGRHg5qgbDHaXyAdZ9y2oKMMZYvLlDypHxHlBxF0N5wGeV YdcYDsH8qkJYodKRXTXzxNHrKGoPIxgQmLip9zjEM9TciJiOpkYDHeAbm7oQXQHu YnRz9DrhYa9GIrd4781Nz2f1yCU1A08Sib8Vb5vgrD3mVxCS7Gy3bIgvOs4mybIK y3GDfLL7Qa/UCTZEh8vXSb1uJYkO6JjrL2+4O6sji++wEh73KkDA0YrST9msGopG BNLoCcZHRMImfZgTFZQdXam6GQyELvbLhRBC+TNDIFpqAIiD0sezhgxtmeOm+VpM C8V7VMylACQ7UXfMiRu5yl990htbkiur/Oedq0VIzjPNNSWpCJtZgKL3t30R1tSh 3SxJXA3JxEZRkcOYJQA+AVT8YhrIt5fB2YqwhIyvSQ9OSs8VzvPEZV5FuVaO6o3K jaSfY65SlQycD+A= =4f4e -----END PGP SIGNATURE----- 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 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) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package fonts-lato. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19616 files and directories currently installed.) Preparing to unpack .../0-fonts-lato_2.0-2.1_all.deb ... Unpacking fonts-lato (2.0-2.1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../1-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package ucf. Preparing to unpack .../2-ucf_3.0043+nmu1_all.deb ... Moving old data out of the way Unpacking ucf (3.0043+nmu1) ... Selecting previously unselected package libdebuginfod-common. Preparing to unpack .../3-libdebuginfod-common_0.188-2.1_all.deb ... Unpacking libdebuginfod-common (0.188-2.1) ... Selecting previously unselected package libpython3.11-minimal:arm64. Preparing to unpack .../4-libpython3.11-minimal_3.11.2-6_arm64.deb ... Unpacking libpython3.11-minimal:arm64 (3.11.2-6) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../5-libexpat1_2.5.0-1_arm64.deb ... Unpacking libexpat1:arm64 (2.5.0-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../6-python3.11-minimal_3.11.2-6_arm64.deb ... Unpacking python3.11-minimal (3.11.2-6) ... Setting up libpython3.11-minimal:arm64 (3.11.2-6) ... Setting up libexpat1:arm64 (2.5.0-1) ... Setting up python3.11-minimal (3.11.2-6) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20043 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.2-1+b1_arm64.deb ... Unpacking python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.0.0_all.deb ... Unpacking media-types (10.0.0) ... Selecting previously unselected package readline-common. Preparing to unpack .../2-readline-common_8.2-1.3_all.deb ... Unpacking readline-common (8.2-1.3) ... Selecting previously unselected package libreadline8:arm64. Preparing to unpack .../3-libreadline8_8.2-1.3_arm64.deb ... Unpacking libreadline8:arm64 (8.2-1.3) ... Selecting previously unselected package libpython3.11-stdlib:arm64. Preparing to unpack .../4-libpython3.11-stdlib_3.11.2-6_arm64.deb ... Unpacking libpython3.11-stdlib:arm64 (3.11.2-6) ... Selecting previously unselected package python3.11. Preparing to unpack .../5-python3.11_3.11.2-6_arm64.deb ... Unpacking python3.11 (3.11.2-6) ... Selecting previously unselected package libpython3-stdlib:arm64. Preparing to unpack .../6-libpython3-stdlib_3.11.2-1+b1_arm64.deb ... Unpacking libpython3-stdlib:arm64 (3.11.2-1+b1) ... Setting up python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20477 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.2-1+b1_arm64.deb ... Unpacking python3 (3.11.2-1+b1) ... Selecting previously unselected package sgml-base. Preparing to unpack .../001-sgml-base_1.31_all.deb ... Unpacking sgml-base (1.31) ... Selecting previously unselected package libproc2-0:arm64. Preparing to unpack .../002-libproc2-0_2%3a4.0.2-3_arm64.deb ... Unpacking libproc2-0:arm64 (2:4.0.2-3) ... Selecting previously unselected package procps. Preparing to unpack .../003-procps_2%3a4.0.2-3_arm64.deb ... Unpacking procps (2:4.0.2-3) ... Selecting previously unselected package openssl. Preparing to unpack .../004-openssl_3.0.8-1_arm64.deb ... Unpacking openssl (3.0.8-1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../005-ca-certificates_20230311_all.deb ... Unpacking ca-certificates (20230311) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../006-libmagic-mgc_1%3a5.44-3_arm64.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../007-libmagic1_1%3a5.44-3_arm64.deb ... Unpacking libmagic1:arm64 (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../008-file_1%3a5.44-3_arm64.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../009-gettext-base_0.21-12_arm64.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../010-libuchardet0_0.0.7-1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../011-groff-base_1.22.4-10_arm64.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../012-bsdextrautils_2.38.1-5+b1_arm64.deb ... Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../013-libpipeline1_1.5.7-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../014-man-db_2.11.2-2_arm64.deb ... Unpacking man-db (2.11.2-2) ... Selecting previously unselected package m4. Preparing to unpack .../015-m4_1.4.19-3_arm64.deb ... Unpacking m4 (1.4.19-3) ... Selecting previously unselected package autoconf. Preparing to unpack .../016-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../017-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../018-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../019-autopoint_0.21-12_all.deb ... Unpacking autopoint (0.21-12) ... Selecting previously unselected package libtcl8.6:arm64. Preparing to unpack .../020-libtcl8.6_8.6.13+dfsg-2_arm64.deb ... Unpacking libtcl8.6:arm64 (8.6.13+dfsg-2) ... Selecting previously unselected package libbrotli1:arm64. Preparing to unpack .../021-libbrotli1_1.0.9-2+b6_arm64.deb ... Unpacking libbrotli1:arm64 (1.0.9-2+b6) ... Selecting previously unselected package libpng16-16:arm64. Preparing to unpack .../022-libpng16-16_1.6.39-2_arm64.deb ... Unpacking libpng16-16:arm64 (1.6.39-2) ... Selecting previously unselected package libfreetype6:arm64. Preparing to unpack .../023-libfreetype6_2.12.1+dfsg-4_arm64.deb ... Unpacking libfreetype6:arm64 (2.12.1+dfsg-4) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../024-fonts-dejavu-core_2.37-6_all.deb ... Unpacking fonts-dejavu-core (2.37-6) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../025-fontconfig-config_2.14.1-4_arm64.deb ... Unpacking fontconfig-config (2.14.1-4) ... Selecting previously unselected package libfontconfig1:arm64. Preparing to unpack .../026-libfontconfig1_2.14.1-4_arm64.deb ... Unpacking libfontconfig1:arm64 (2.14.1-4) ... Selecting previously unselected package libxau6:arm64. Preparing to unpack .../027-libxau6_1%3a1.0.9-1_arm64.deb ... Unpacking libxau6:arm64 (1:1.0.9-1) ... Selecting previously unselected package libbsd0:arm64. Preparing to unpack .../028-libbsd0_0.11.7-2_arm64.deb ... Unpacking libbsd0:arm64 (0.11.7-2) ... Selecting previously unselected package libxdmcp6:arm64. Preparing to unpack .../029-libxdmcp6_1%3a1.1.2-3_arm64.deb ... Unpacking libxdmcp6:arm64 (1:1.1.2-3) ... Selecting previously unselected package libxcb1:arm64. Preparing to unpack .../030-libxcb1_1.15-1_arm64.deb ... Unpacking libxcb1:arm64 (1.15-1) ... Selecting previously unselected package libx11-data. Preparing to unpack .../031-libx11-data_2%3a1.8.4-2_all.deb ... Unpacking libx11-data (2:1.8.4-2) ... Selecting previously unselected package libx11-6:arm64. Preparing to unpack .../032-libx11-6_2%3a1.8.4-2_arm64.deb ... Unpacking libx11-6:arm64 (2:1.8.4-2) ... Selecting previously unselected package libxrender1:arm64. Preparing to unpack .../033-libxrender1_1%3a0.9.10-1.1_arm64.deb ... Unpacking libxrender1:arm64 (1:0.9.10-1.1) ... Selecting previously unselected package libxft2:arm64. Preparing to unpack .../034-libxft2_2.3.6-1_arm64.deb ... Unpacking libxft2:arm64 (2.3.6-1) ... Selecting previously unselected package libxext6:arm64. Preparing to unpack .../035-libxext6_2%3a1.3.4-1+b1_arm64.deb ... Unpacking libxext6:arm64 (2:1.3.4-1+b1) ... Selecting previously unselected package x11-common. Preparing to unpack .../036-x11-common_1%3a7.7+23_all.deb ... Unpacking x11-common (1:7.7+23) ... Selecting previously unselected package libxss1:arm64. Preparing to unpack .../037-libxss1_1%3a1.2.3-1_arm64.deb ... Unpacking libxss1:arm64 (1:1.2.3-1) ... Selecting previously unselected package libtk8.6:arm64. Preparing to unpack .../038-libtk8.6_8.6.13-2_arm64.deb ... Unpacking libtk8.6:arm64 (8.6.13-2) ... Selecting previously unselected package tk8.6-blt2.5. Preparing to unpack .../039-tk8.6-blt2.5_2.5.3+dfsg-4.1_arm64.deb ... Unpacking tk8.6-blt2.5 (2.5.3+dfsg-4.1) ... Selecting previously unselected package blt. Preparing to unpack .../040-blt_2.5.3+dfsg-4.1_arm64.deb ... Unpacking blt (2.5.3+dfsg-4.1) ... Selecting previously unselected package cython3. Preparing to unpack .../041-cython3_0.29.32-2+b1_arm64.deb ... Unpacking cython3 (0.29.32-2+b1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../042-libdebhelper-perl_13.11.4_all.deb ... Unpacking libdebhelper-perl (13.11.4) ... Selecting previously unselected package libtool. Preparing to unpack .../043-libtool_2.4.7-5_all.deb ... Unpacking libtool (2.4.7-5) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../044-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../045-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../046-libsub-override-perl_0.09-4_all.deb ... Unpacking libsub-override-perl (0.09-4) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../047-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../048-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1:arm64. Preparing to unpack .../049-libelf1_0.188-2.1_arm64.deb ... Unpacking libelf1:arm64 (0.188-2.1) ... Selecting previously unselected package dwz. Preparing to unpack .../050-dwz_0.15-1_arm64.deb ... Unpacking dwz (0.15-1) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../051-libicu72_72.1-3_arm64.deb ... Unpacking libicu72:arm64 (72.1-3) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../052-libxml2_2.9.14+dfsg-1.1+b3_arm64.deb ... Unpacking libxml2:arm64 (2.9.14+dfsg-1.1+b3) ... Selecting previously unselected package gettext. Preparing to unpack .../053-gettext_0.21-12_arm64.deb ... Unpacking gettext (0.21-12) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../054-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../055-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../056-debhelper_13.11.4_all.deb ... Unpacking debhelper (13.11.4) ... Selecting previously unselected package python3-lib2to3. Preparing to unpack .../057-python3-lib2to3_3.11.2-2_all.deb ... Unpacking python3-lib2to3 (3.11.2-2) ... Selecting previously unselected package python3-distutils. Preparing to unpack .../058-python3-distutils_3.11.2-2_all.deb ... Unpacking python3-distutils (3.11.2-2) ... Selecting previously unselected package dh-python. Preparing to unpack .../059-dh-python_5.20230130_all.deb ... Unpacking dh-python (5.20230130) ... Selecting previously unselected package xml-core. Preparing to unpack .../060-xml-core_0.18+nmu1_all.deb ... Unpacking xml-core (0.18+nmu1) ... Selecting previously unselected package docutils-common. Preparing to unpack .../061-docutils-common_0.19+dfsg-6_all.deb ... Unpacking docutils-common (0.19+dfsg-6) ... Selecting previously unselected package fonts-font-awesome. Preparing to unpack .../062-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... Selecting previously unselected package fonts-lyx. Preparing to unpack .../063-fonts-lyx_2.3.7-1_all.deb ... Unpacking fonts-lyx (2.3.7-1) ... Selecting previously unselected package fonts-mathjax. Preparing to unpack .../064-fonts-mathjax_2.7.9+dfsg-1_all.deb ... Unpacking fonts-mathjax (2.7.9+dfsg-1) ... Selecting previously unselected package libdw1:arm64. Preparing to unpack .../065-libdw1_0.188-2.1_arm64.deb ... Unpacking libdw1:arm64 (0.188-2.1) ... Selecting previously unselected package libglib2.0-0:arm64. Preparing to unpack .../066-libglib2.0-0_2.74.6-1_arm64.deb ... Unpacking libglib2.0-0:arm64 (2.74.6-1) ... Selecting previously unselected package libbabeltrace1:arm64. Preparing to unpack .../067-libbabeltrace1_1.5.11-1+b2_arm64.deb ... Unpacking libbabeltrace1:arm64 (1.5.11-1+b2) ... Selecting previously unselected package libsasl2-modules-db:arm64. Preparing to unpack .../068-libsasl2-modules-db_2.1.28+dfsg-10_arm64.deb ... Unpacking libsasl2-modules-db:arm64 (2.1.28+dfsg-10) ... Selecting previously unselected package libsasl2-2:arm64. Preparing to unpack .../069-libsasl2-2_2.1.28+dfsg-10_arm64.deb ... Unpacking libsasl2-2:arm64 (2.1.28+dfsg-10) ... Selecting previously unselected package libldap-2.5-0:arm64. Preparing to unpack .../070-libldap-2.5-0_2.5.13+dfsg-5_arm64.deb ... Unpacking libldap-2.5-0:arm64 (2.5.13+dfsg-5) ... Selecting previously unselected package libnghttp2-14:arm64. Preparing to unpack .../071-libnghttp2-14_1.52.0-1_arm64.deb ... Unpacking libnghttp2-14:arm64 (1.52.0-1) ... Selecting previously unselected package libpsl5:arm64. Preparing to unpack .../072-libpsl5_0.21.2-1_arm64.deb ... Unpacking libpsl5:arm64 (0.21.2-1) ... Selecting previously unselected package librtmp1:arm64. Preparing to unpack .../073-librtmp1_2.4+20151223.gitfa8646d.1-2+b2_arm64.deb ... Unpacking librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b2) ... Selecting previously unselected package libssh2-1:arm64. Preparing to unpack .../074-libssh2-1_1.10.0-3+b1_arm64.deb ... Unpacking libssh2-1:arm64 (1.10.0-3+b1) ... Selecting previously unselected package libcurl3-gnutls:arm64. Preparing to unpack .../075-libcurl3-gnutls_7.88.1-8_arm64.deb ... Unpacking libcurl3-gnutls:arm64 (7.88.1-8) ... Selecting previously unselected package libdebuginfod1:arm64. Preparing to unpack .../076-libdebuginfod1_0.188-2.1_arm64.deb ... Unpacking libdebuginfod1:arm64 (0.188-2.1) ... Selecting previously unselected package libpython3.11:arm64. Preparing to unpack .../077-libpython3.11_3.11.2-6_arm64.deb ... Unpacking libpython3.11:arm64 (3.11.2-6) ... Selecting previously unselected package libsource-highlight-common. Preparing to unpack .../078-libsource-highlight-common_3.1.9-4.2_all.deb ... Unpacking libsource-highlight-common (3.1.9-4.2) ... Selecting previously unselected package libboost-regex1.74.0:arm64. Preparing to unpack .../079-libboost-regex1.74.0_1.74.0+ds1-20_arm64.deb ... Unpacking libboost-regex1.74.0:arm64 (1.74.0+ds1-20) ... Selecting previously unselected package libsource-highlight4v5:arm64. Preparing to unpack .../080-libsource-highlight4v5_3.1.9-4.2+b3_arm64.deb ... Unpacking libsource-highlight4v5:arm64 (3.1.9-4.2+b3) ... Selecting previously unselected package gdb. Preparing to unpack .../081-gdb_13.1-2_arm64.deb ... Unpacking gdb (13.1-2) ... Selecting previously unselected package libaec0:arm64. Preparing to unpack .../082-libaec0_1.0.6-1+b1_arm64.deb ... Unpacking libaec0:arm64 (1.0.6-1+b1) ... Selecting previously unselected package libblas3:arm64. Preparing to unpack .../083-libblas3_3.11.0-2_arm64.deb ... Unpacking libblas3:arm64 (3.11.0-2) ... Selecting previously unselected package libsnappy1v5:arm64. Preparing to unpack .../084-libsnappy1v5_1.1.9-3_arm64.deb ... Unpacking libsnappy1v5:arm64 (1.1.9-3) ... Selecting previously unselected package libblosc1:arm64. Preparing to unpack .../085-libblosc1_1.21.3+ds-1_arm64.deb ... Unpacking libblosc1:arm64 (1.21.3+ds-1) ... Selecting previously unselected package libboost1.74-dev:arm64. Preparing to unpack .../086-libboost1.74-dev_1.74.0+ds1-20_arm64.deb ... Unpacking libboost1.74-dev:arm64 (1.74.0+ds1-20) ... Selecting previously unselected package libboost-dev:arm64. Preparing to unpack .../087-libboost-dev_1.74.0.3_arm64.deb ... Unpacking libboost-dev:arm64 (1.74.0.3) ... Selecting previously unselected package libcurl4:arm64. Preparing to unpack .../088-libcurl4_7.88.1-8_arm64.deb ... Unpacking libcurl4:arm64 (7.88.1-8) ... Selecting previously unselected package libdeflate0:arm64. Preparing to unpack .../089-libdeflate0_1.14-1_arm64.deb ... Unpacking libdeflate0:arm64 (1.14-1) ... Selecting previously unselected package libexpat1-dev:arm64. Preparing to unpack .../090-libexpat1-dev_2.5.0-1_arm64.deb ... Unpacking libexpat1-dev:arm64 (2.5.0-1) ... Selecting previously unselected package libfribidi0:arm64. Preparing to unpack .../091-libfribidi0_1.0.8-2.1_arm64.deb ... Unpacking libfribidi0:arm64 (1.0.8-2.1) ... Selecting previously unselected package libgfortran5:arm64. Preparing to unpack .../092-libgfortran5_12.2.0-14_arm64.deb ... Unpacking libgfortran5:arm64 (12.2.0-14) ... Selecting previously unselected package libgraphite2-3:arm64. Preparing to unpack .../093-libgraphite2-3_1.3.14-1_arm64.deb ... Unpacking libgraphite2-3:arm64 (1.3.14-1) ... Selecting previously unselected package libharfbuzz0b:arm64. Preparing to unpack .../094-libharfbuzz0b_6.0.0+dfsg-3_arm64.deb ... Unpacking libharfbuzz0b:arm64 (6.0.0+dfsg-3) ... Selecting previously unselected package libsz2:arm64. Preparing to unpack .../095-libsz2_1.0.6-1+b1_arm64.deb ... Unpacking libsz2:arm64 (1.0.6-1+b1) ... Selecting previously unselected package libhdf5-103-1:arm64. Preparing to unpack .../096-libhdf5-103-1_1.10.8+repack1-1_arm64.deb ... Unpacking libhdf5-103-1:arm64 (1.10.8+repack1-1) ... Selecting previously unselected package libimagequant0:arm64. Preparing to unpack .../097-libimagequant0_2.17.0-1_arm64.deb ... Unpacking libimagequant0:arm64 (2.17.0-1) ... Selecting previously unselected package libjbig0:arm64. Preparing to unpack .../098-libjbig0_2.1-6.1_arm64.deb ... Unpacking libjbig0:arm64 (2.1-6.1) ... Selecting previously unselected package libjpeg62-turbo:arm64. Preparing to unpack .../099-libjpeg62-turbo_1%3a2.1.5-2_arm64.deb ... Unpacking libjpeg62-turbo:arm64 (1:2.1.5-2) ... Selecting previously unselected package libjs-jquery. Preparing to unpack .../100-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Selecting previously unselected package libjs-jquery-ui. Preparing to unpack .../101-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... Selecting previously unselected package libjs-mathjax. Preparing to unpack .../102-libjs-mathjax_2.7.9+dfsg-1_all.deb ... Unpacking libjs-mathjax (2.7.9+dfsg-1) ... Selecting previously unselected package libjs-underscore. Preparing to unpack .../103-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Selecting previously unselected package libjs-sphinxdoc. Preparing to unpack .../104-libjs-sphinxdoc_5.3.0-4_all.deb ... Unpacking libjs-sphinxdoc (5.3.0-4) ... Selecting previously unselected package libjson-perl. Preparing to unpack .../105-libjson-perl_4.10000-1_all.deb ... Unpacking libjson-perl (4.10000-1) ... Selecting previously unselected package libopenblas0-pthread:arm64. Preparing to unpack .../106-libopenblas0-pthread_0.3.21+ds-4_arm64.deb ... Unpacking libopenblas0-pthread:arm64 (0.3.21+ds-4) ... Selecting previously unselected package liblapack3:arm64. Preparing to unpack .../107-liblapack3_3.11.0-2_arm64.deb ... Unpacking liblapack3:arm64 (3.11.0-2) ... Selecting previously unselected package liblbfgsb0:arm64. Preparing to unpack .../108-liblbfgsb0_3.0+dfsg.4-1_arm64.deb ... Unpacking liblbfgsb0:arm64 (3.0+dfsg.4-1) ... Selecting previously unselected package liblcms2-2:arm64. Preparing to unpack .../109-liblcms2-2_2.14-2_arm64.deb ... Unpacking liblcms2-2:arm64 (2.14-2) ... Selecting previously unselected package liblerc4:arm64. Preparing to unpack .../110-liblerc4_4.0.0+ds-2_arm64.deb ... Unpacking liblerc4:arm64 (4.0.0+ds-2) ... Selecting previously unselected package liblzo2-2:arm64. Preparing to unpack .../111-liblzo2-2_2.10-2_arm64.deb ... Unpacking liblzo2-2:arm64 (2.10-2) ... Selecting previously unselected package libnorm1:arm64. Preparing to unpack .../112-libnorm1_1.5.9+dfsg-2_arm64.deb ... Unpacking libnorm1:arm64 (1.5.9+dfsg-2) ... Selecting previously unselected package libopenblas0:arm64. Preparing to unpack .../113-libopenblas0_0.3.21+ds-4_arm64.deb ... Unpacking libopenblas0:arm64 (0.3.21+ds-4) ... Selecting previously unselected package libopenblas-pthread-dev:arm64. Preparing to unpack .../114-libopenblas-pthread-dev_0.3.21+ds-4_arm64.deb ... Unpacking libopenblas-pthread-dev:arm64 (0.3.21+ds-4) ... Selecting previously unselected package libopenblas-dev:arm64. Preparing to unpack .../115-libopenblas-dev_0.3.21+ds-4_arm64.deb ... Unpacking libopenblas-dev:arm64 (0.3.21+ds-4) ... Selecting previously unselected package libopenjp2-7:arm64. Preparing to unpack .../116-libopenjp2-7_2.5.0-1+b1_arm64.deb ... Unpacking libopenjp2-7:arm64 (2.5.0-1+b1) ... Selecting previously unselected package libpgm-5.3-0:arm64. Preparing to unpack .../117-libpgm-5.3-0_5.3.128~dfsg-2_arm64.deb ... Unpacking libpgm-5.3-0:arm64 (5.3.128~dfsg-2) ... Selecting previously unselected package zlib1g-dev:arm64. Preparing to unpack .../118-zlib1g-dev_1%3a1.2.13.dfsg-1_arm64.deb ... Unpacking zlib1g-dev:arm64 (1:1.2.13.dfsg-1) ... Selecting previously unselected package libpython3.11-dev:arm64. Preparing to unpack .../119-libpython3.11-dev_3.11.2-6_arm64.deb ... Unpacking libpython3.11-dev:arm64 (3.11.2-6) ... Selecting previously unselected package libpython3-dev:arm64. Preparing to unpack .../120-libpython3-dev_3.11.2-1+b1_arm64.deb ... Unpacking libpython3-dev:arm64 (3.11.2-1+b1) ... Selecting previously unselected package libpython3-all-dev:arm64. Preparing to unpack .../121-libpython3-all-dev_3.11.2-1+b1_arm64.deb ... Unpacking libpython3-all-dev:arm64 (3.11.2-1+b1) ... Selecting previously unselected package libqhull-r8.0:arm64. Preparing to unpack .../122-libqhull-r8.0_2020.2-5_arm64.deb ... Unpacking libqhull-r8.0:arm64 (2020.2-5) ... Selecting previously unselected package libraqm0:arm64. Preparing to unpack .../123-libraqm0_0.7.0-4.1_arm64.deb ... Unpacking libraqm0:arm64 (0.7.0-4.1) ... Selecting previously unselected package libsodium23:arm64. Preparing to unpack .../124-libsodium23_1.0.18-1_arm64.deb ... Unpacking libsodium23:arm64 (1.0.18-1) ... Selecting previously unselected package libwebp7:arm64. Preparing to unpack .../125-libwebp7_1.2.4-0.1_arm64.deb ... Unpacking libwebp7:arm64 (1.2.4-0.1) ... Selecting previously unselected package libtiff6:arm64. Preparing to unpack .../126-libtiff6_4.5.0-5_arm64.deb ... Unpacking libtiff6:arm64 (4.5.0-5) ... Selecting previously unselected package libwebpdemux2:arm64. Preparing to unpack .../127-libwebpdemux2_1.2.4-0.1_arm64.deb ... Unpacking libwebpdemux2:arm64 (1.2.4-0.1) ... Selecting previously unselected package libwebpmux3:arm64. Preparing to unpack .../128-libwebpmux3_1.2.4-0.1_arm64.deb ... Unpacking libwebpmux3:arm64 (1.2.4-0.1) ... Selecting previously unselected package libxsimd-dev:arm64. Preparing to unpack .../129-libxsimd-dev_8.1.0-7_arm64.deb ... Unpacking libxsimd-dev:arm64 (8.1.0-7) ... Selecting previously unselected package libxslt1.1:arm64. Preparing to unpack .../130-libxslt1.1_1.1.35-1_arm64.deb ... Unpacking libxslt1.1:arm64 (1.1.35-1) ... Selecting previously unselected package libzmq5:arm64. Preparing to unpack .../131-libzmq5_4.3.4-6_arm64.deb ... Unpacking libzmq5:arm64 (4.3.4-6) ... Selecting previously unselected package python-babel-localedata. Preparing to unpack .../132-python-babel-localedata_2.10.3-1_all.deb ... Unpacking python-babel-localedata (2.10.3-1) ... Selecting previously unselected package python-matplotlib-data. Preparing to unpack .../133-python-matplotlib-data_3.6.3-1_all.deb ... Unpacking python-matplotlib-data (3.6.3-1) ... Selecting previously unselected package python-tables-data. Preparing to unpack .../134-python-tables-data_3.7.0-5_all.deb ... Unpacking python-tables-data (3.7.0-5) ... Selecting previously unselected package python-tinycss2-common. Preparing to unpack .../135-python-tinycss2-common_1.2.1-2_all.deb ... Unpacking python-tinycss2-common (1.2.1-2) ... Selecting previously unselected package python3-alabaster. Preparing to unpack .../136-python3-alabaster_0.7.12-1_all.deb ... Unpacking python3-alabaster (0.7.12-1) ... Selecting previously unselected package python3-all. Preparing to unpack .../137-python3-all_3.11.2-1+b1_arm64.deb ... Unpacking python3-all (3.11.2-1+b1) ... Selecting previously unselected package python3.11-dev. Preparing to unpack .../138-python3.11-dev_3.11.2-6_arm64.deb ... Unpacking python3.11-dev (3.11.2-6) ... Selecting previously unselected package python3-dev. Preparing to unpack .../139-python3-dev_3.11.2-1+b1_arm64.deb ... Unpacking python3-dev (3.11.2-1+b1) ... Selecting previously unselected package python3-all-dev. Preparing to unpack .../140-python3-all-dev_3.11.2-1+b1_arm64.deb ... Unpacking python3-all-dev (3.11.2-1+b1) ... Selecting previously unselected package python3-appdirs. Preparing to unpack .../141-python3-appdirs_1.4.4-3_all.deb ... Unpacking python3-appdirs (1.4.4-3) ... Selecting previously unselected package python3-six. Preparing to unpack .../142-python3-six_1.16.0-4_all.deb ... Unpacking python3-six (1.16.0-4) ... Selecting previously unselected package python3-asttokens. Preparing to unpack .../143-python3-asttokens_2.2.1-1_all.deb ... Unpacking python3-asttokens (2.2.1-1) ... Selecting previously unselected package python3-astunparse. Preparing to unpack .../144-python3-astunparse_1.6.3-2_all.deb ... Unpacking python3-astunparse (1.6.3-2) ... Selecting previously unselected package python3-attr. Preparing to unpack .../145-python3-attr_22.2.0-1_all.deb ... Unpacking python3-attr (22.2.0-1) ... Selecting previously unselected package python3-pkg-resources. Preparing to unpack .../146-python3-pkg-resources_66.1.1-1_all.deb ... Unpacking python3-pkg-resources (66.1.1-1) ... Selecting previously unselected package python3-tz. Preparing to unpack .../147-python3-tz_2022.7.1-3_all.deb ... Unpacking python3-tz (2022.7.1-3) ... Selecting previously unselected package python3-babel. Preparing to unpack .../148-python3-babel_2.10.3-1_all.deb ... Unpacking python3-babel (2.10.3-1) ... Selecting previously unselected package python3-backcall. Preparing to unpack .../149-python3-backcall_0.2.0-4_all.deb ... Unpacking python3-backcall (0.2.0-4) ... Selecting previously unselected package python3-gast. Preparing to unpack .../150-python3-gast_0.5.2-2_all.deb ... Unpacking python3-gast (0.5.2-2) ... Selecting previously unselected package python3-beniget. Preparing to unpack .../151-python3-beniget_0.4.1-3_all.deb ... Unpacking python3-beniget (0.4.1-3) ... Selecting previously unselected package python3-webencodings. Preparing to unpack .../152-python3-webencodings_0.5.1-5_all.deb ... Unpacking python3-webencodings (0.5.1-5) ... Selecting previously unselected package python3-html5lib. Preparing to unpack .../153-python3-html5lib_1.1-3_all.deb ... Unpacking python3-html5lib (1.1-3) ... Selecting previously unselected package python3-bleach. Preparing to unpack .../154-python3-bleach_5.0.1-2_all.deb ... Unpacking python3-bleach (5.0.1-2) ... Selecting previously unselected package python3-brotli. Preparing to unpack .../155-python3-brotli_1.0.9-2+b6_arm64.deb ... Unpacking python3-brotli (1.0.9-2+b6) ... Selecting previously unselected package python3-soupsieve. Preparing to unpack .../156-python3-soupsieve_2.3.2-1_all.deb ... Unpacking python3-soupsieve (2.3.2-1) ... Selecting previously unselected package python3-bs4. Preparing to unpack .../157-python3-bs4_4.11.2-2_all.deb ... Unpacking python3-bs4 (4.11.2-2) ... Selecting previously unselected package python3-bytecode. Preparing to unpack .../158-python3-bytecode_0.14.0-2_all.deb ... Unpacking python3-bytecode (0.14.0-2) ... Selecting previously unselected package python3-certifi. Preparing to unpack .../159-python3-certifi_2022.9.24-1_all.deb ... Unpacking python3-certifi (2022.9.24-1) ... Selecting previously unselected package python3-cffi-backend:arm64. Preparing to unpack .../160-python3-cffi-backend_1.15.1-5+b1_arm64.deb ... Unpacking python3-cffi-backend:arm64 (1.15.1-5+b1) ... Selecting previously unselected package python3-chardet. Preparing to unpack .../161-python3-chardet_5.1.0+dfsg-2_all.deb ... Unpacking python3-chardet (5.1.0+dfsg-2) ... Selecting previously unselected package python3-charset-normalizer. Preparing to unpack .../162-python3-charset-normalizer_3.0.1-2_all.deb ... Unpacking python3-charset-normalizer (3.0.1-2) ... Selecting previously unselected package python3-numpy. Preparing to unpack .../163-python3-numpy_1%3a1.24.2-1_arm64.deb ... Unpacking python3-numpy (1:1.24.2-1) ... Selecting previously unselected package python3-contourpy. Preparing to unpack .../164-python3-contourpy_1.0.7-1+b1_arm64.deb ... Unpacking python3-contourpy (1.0.7-1+b1) ... Selecting previously unselected package python3-coverage. Preparing to unpack .../165-python3-coverage_6.5.0+dfsg1-2+b1_arm64.deb ... Unpacking python3-coverage (6.5.0+dfsg1-2+b1) ... Selecting previously unselected package python3-cycler. Preparing to unpack .../166-python3-cycler_0.11.0-1_all.deb ... Unpacking python3-cycler (0.11.0-1) ... Selecting previously unselected package python3-dateutil. Preparing to unpack .../167-python3-dateutil_2.8.2-2_all.deb ... Unpacking python3-dateutil (2.8.2-2) ... Selecting previously unselected package python3-pydevd. Preparing to unpack .../168-python3-pydevd_2.9.5+ds-4_arm64.deb ... Unpacking python3-pydevd (2.9.5+ds-4) ... Selecting previously unselected package python3-debugpy. Preparing to unpack .../169-python3-debugpy_1.6.6+ds-1_all.deb ... Unpacking python3-debugpy (1.6.6+ds-1) ... Selecting previously unselected package python3-decorator. Preparing to unpack .../170-python3-decorator_5.1.1-3_all.deb ... Unpacking python3-decorator (5.1.1-3) ... Selecting previously unselected package python3-defusedxml. Preparing to unpack .../171-python3-defusedxml_0.7.1-2_all.deb ... Unpacking python3-defusedxml (0.7.1-2) ... Selecting previously unselected package python3-roman. Preparing to unpack .../172-python3-roman_3.3-3_all.deb ... Unpacking python3-roman (3.3-3) ... Selecting previously unselected package python3-docutils. Preparing to unpack .../173-python3-docutils_0.19+dfsg-6_all.deb ... Unpacking python3-docutils (0.19+dfsg-6) ... Selecting previously unselected package python3-entrypoints. Preparing to unpack .../174-python3-entrypoints_0.4-2_all.deb ... Unpacking python3-entrypoints (0.4-2) ... Selecting previously unselected package python3-executing. Preparing to unpack .../175-python3-executing_1.2.0-2_all.deb ... Unpacking python3-executing (1.2.0-2) ... Selecting previously unselected package python3-fastjsonschema. Preparing to unpack .../176-python3-fastjsonschema_2.16.3-2_all.deb ... Unpacking python3-fastjsonschema (2.16.3-2) ... Selecting previously unselected package python3-ply. Preparing to unpack .../177-python3-ply_3.11-5_all.deb ... Unpacking python3-ply (3.11-5) ... Selecting previously unselected package python3-pythran. Preparing to unpack .../178-python3-pythran_0.11.0+ds-7_arm64.deb ... Unpacking python3-pythran (0.11.0+ds-7) ... Selecting previously unselected package python3-scipy. Preparing to unpack .../179-python3-scipy_1.10.1-2_arm64.deb ... Unpacking python3-scipy (1.10.1-2) ... Selecting previously unselected package python3-ufolib2. Preparing to unpack .../180-python3-ufolib2_0.14.0+dfsg1-1_all.deb ... Unpacking python3-ufolib2 (0.14.0+dfsg1-1) ... Selecting previously unselected package python3-mpmath. Preparing to unpack .../181-python3-mpmath_1.2.1-2_all.deb ... Unpacking python3-mpmath (1.2.1-2) ... Selecting previously unselected package python3-sympy. Preparing to unpack .../182-python3-sympy_1.11.1-1_all.deb ... Unpacking python3-sympy (1.11.1-1) ... Selecting previously unselected package python3-fs. Preparing to unpack .../183-python3-fs_2.4.16-2_all.deb ... Unpacking python3-fs (2.4.16-2) ... Selecting previously unselected package python3-lxml:arm64. Preparing to unpack .../184-python3-lxml_4.9.2-1+b1_arm64.deb ... Unpacking python3-lxml:arm64 (4.9.2-1+b1) ... Selecting previously unselected package python3-lz4. Preparing to unpack .../185-python3-lz4_4.0.2+dfsg-1+b2_arm64.deb ... Unpacking python3-lz4 (4.0.2+dfsg-1+b2) ... Selecting previously unselected package unicode-data. Preparing to unpack .../186-unicode-data_15.0.0-1_all.deb ... Unpacking unicode-data (15.0.0-1) ... Selecting previously unselected package python3-fonttools. Preparing to unpack .../187-python3-fonttools_4.38.0-1+b1_arm64.deb ... Unpacking python3-fonttools (4.38.0-1+b1) ... Selecting previously unselected package python3-idna. Preparing to unpack .../188-python3-idna_3.3-1_all.deb ... Unpacking python3-idna (3.3-1) ... Selecting previously unselected package python3-imagesize. Preparing to unpack .../189-python3-imagesize_1.4.1-1_all.deb ... Unpacking python3-imagesize (1.4.1-1) ... Selecting previously unselected package python3-parso. Preparing to unpack .../190-python3-parso_0.8.3-1_all.deb ... Unpacking python3-parso (0.8.3-1) ... Selecting previously unselected package python3-jedi. Preparing to unpack .../191-python3-jedi_0.18.2-1_all.deb ... Unpacking python3-jedi (0.18.2-1) ... Selecting previously unselected package python3-traitlets. Preparing to unpack .../192-python3-traitlets_5.5.0-1_all.deb ... Unpacking python3-traitlets (5.5.0-1) ... Selecting previously unselected package python3-matplotlib-inline. Preparing to unpack .../193-python3-matplotlib-inline_0.1.6-2_all.deb ... Unpacking python3-matplotlib-inline (0.1.6-2) ... Selecting previously unselected package python3-ptyprocess. Preparing to unpack .../194-python3-ptyprocess_0.7.0-5_all.deb ... Unpacking python3-ptyprocess (0.7.0-5) ... Selecting previously unselected package python3-pexpect. Preparing to unpack .../195-python3-pexpect_4.8.0-4_all.deb ... Unpacking python3-pexpect (4.8.0-4) ... Selecting previously unselected package python3-pickleshare. Preparing to unpack .../196-python3-pickleshare_0.7.5-5_all.deb ... Unpacking python3-pickleshare (0.7.5-5) ... Selecting previously unselected package python3-wcwidth. Preparing to unpack .../197-python3-wcwidth_0.2.5+dfsg1-1.1_all.deb ... Unpacking python3-wcwidth (0.2.5+dfsg1-1.1) ... Selecting previously unselected package python3-prompt-toolkit. Preparing to unpack .../198-python3-prompt-toolkit_3.0.36-2_all.deb ... Unpacking python3-prompt-toolkit (3.0.36-2) ... Selecting previously unselected package python3-pygments. Preparing to unpack .../199-python3-pygments_2.14.0+dfsg-1_all.deb ... Unpacking python3-pygments (2.14.0+dfsg-1) ... Selecting previously unselected package python3-pure-eval. Preparing to unpack .../200-python3-pure-eval_0.2.2-1_all.deb ... Unpacking python3-pure-eval (0.2.2-1) ... Selecting previously unselected package python3-stack-data. Preparing to unpack .../201-python3-stack-data_0.6.2-3_all.deb ... Unpacking python3-stack-data (0.6.2-3) ... Selecting previously unselected package python3-setuptools. Preparing to unpack .../202-python3-setuptools_66.1.1-1_all.deb ... Unpacking python3-setuptools (66.1.1-1) ... Selecting previously unselected package python3-ipython. Preparing to unpack .../203-python3-ipython_8.5.0-4_all.deb ... Unpacking python3-ipython (8.5.0-4) ... Selecting previously unselected package python3-jupyter-core. Preparing to unpack .../204-python3-jupyter-core_4.12.0-1_all.deb ... Unpacking python3-jupyter-core (4.12.0-1) ... Selecting previously unselected package python3-nest-asyncio. Preparing to unpack .../205-python3-nest-asyncio_1.5.4-1_all.deb ... Unpacking python3-nest-asyncio (1.5.4-1) ... Selecting previously unselected package python3-tornado. Preparing to unpack .../206-python3-tornado_6.2.0-3_arm64.deb ... Unpacking python3-tornado (6.2.0-3) ... Selecting previously unselected package python3-py. Preparing to unpack .../207-python3-py_1.11.0-1_all.deb ... Unpacking python3-py (1.11.0-1) ... Selecting previously unselected package python3-zmq. Preparing to unpack .../208-python3-zmq_24.0.1-4+b1_arm64.deb ... Unpacking python3-zmq (24.0.1-4+b1) ... Selecting previously unselected package python3-jupyter-client. Preparing to unpack .../209-python3-jupyter-client_7.4.9-2_all.deb ... Unpacking python3-jupyter-client (7.4.9-2) ... Selecting previously unselected package python3-packaging. Preparing to unpack .../210-python3-packaging_23.0-1_all.deb ... Unpacking python3-packaging (23.0-1) ... Selecting previously unselected package python3-psutil. Preparing to unpack .../211-python3-psutil_5.9.4-1+b1_arm64.deb ... Unpacking python3-psutil (5.9.4-1+b1) ... Selecting previously unselected package python3-ipykernel. Preparing to unpack .../212-python3-ipykernel_6.17.0-1_all.deb ... Unpacking python3-ipykernel (6.17.0-1) ... Selecting previously unselected package python3-markupsafe. Preparing to unpack .../213-python3-markupsafe_2.1.2-1+b1_arm64.deb ... Unpacking python3-markupsafe (2.1.2-1+b1) ... Selecting previously unselected package python3-jinja2. Preparing to unpack .../214-python3-jinja2_3.1.2-1_all.deb ... Unpacking python3-jinja2 (3.1.2-1) ... Selecting previously unselected package python3-joblib. Preparing to unpack .../215-python3-joblib_1.2.0-4_all.deb ... Unpacking python3-joblib (1.2.0-4) ... Selecting previously unselected package python3-pyrsistent:arm64. Preparing to unpack .../216-python3-pyrsistent_0.18.1-1+b3_arm64.deb ... Unpacking python3-pyrsistent:arm64 (0.18.1-1+b3) ... Selecting previously unselected package python3-jsonschema. Preparing to unpack .../217-python3-jsonschema_4.10.3-1_all.deb ... Unpacking python3-jsonschema (4.10.3-1) ... Selecting previously unselected package python3-jupyterlab-pygments. Preparing to unpack .../218-python3-jupyterlab-pygments_0.2.2-3_all.deb ... Unpacking python3-jupyterlab-pygments (0.2.2-3) ... Selecting previously unselected package python3-kiwisolver. Preparing to unpack .../219-python3-kiwisolver_1.4.4-1+b1_arm64.deb ... Unpacking python3-kiwisolver (1.4.4-1+b1) ... Selecting previously unselected package python3-pil:arm64. Preparing to unpack .../220-python3-pil_9.4.0-1.1+b1_arm64.deb ... Unpacking python3-pil:arm64 (9.4.0-1.1+b1) ... Selecting previously unselected package python3-tk:arm64. Preparing to unpack .../221-python3-tk_3.11.2-2_arm64.deb ... Unpacking python3-tk:arm64 (3.11.2-2) ... Selecting previously unselected package python3-pil.imagetk:arm64. Preparing to unpack .../222-python3-pil.imagetk_9.4.0-1.1+b1_arm64.deb ... Unpacking python3-pil.imagetk:arm64 (9.4.0-1.1+b1) ... Selecting previously unselected package python3-pyparsing. Preparing to unpack .../223-python3-pyparsing_3.0.9-1_all.deb ... Unpacking python3-pyparsing (3.0.9-1) ... Selecting previously unselected package python3-matplotlib. Preparing to unpack .../224-python3-matplotlib_3.6.3-1+b1_arm64.deb ... Unpacking python3-matplotlib (3.6.3-1+b1) ... Selecting previously unselected package sphinx-rtd-theme-common. Preparing to unpack .../225-sphinx-rtd-theme-common_1.2.0+dfsg-1_all.deb ... Unpacking sphinx-rtd-theme-common (1.2.0+dfsg-1) ... Selecting previously unselected package sphinx-common. Preparing to unpack .../226-sphinx-common_5.3.0-4_all.deb ... Unpacking sphinx-common (5.3.0-4) ... Selecting previously unselected package python3-urllib3. Preparing to unpack .../227-python3-urllib3_1.26.12-1_all.deb ... Unpacking python3-urllib3 (1.26.12-1) ... Selecting previously unselected package python3-requests. Preparing to unpack .../228-python3-requests_2.28.1+dfsg-1_all.deb ... Unpacking python3-requests (2.28.1+dfsg-1) ... Selecting previously unselected package python3-snowballstemmer. Preparing to unpack .../229-python3-snowballstemmer_2.2.0-2_all.deb ... Unpacking python3-snowballstemmer (2.2.0-2) ... Selecting previously unselected package python3-sphinx. Preparing to unpack .../230-python3-sphinx_5.3.0-4_all.deb ... Unpacking python3-sphinx (5.3.0-4) ... Selecting previously unselected package python3-sphinx-rtd-theme. Preparing to unpack .../231-python3-sphinx-rtd-theme_1.2.0+dfsg-1_all.deb ... Unpacking python3-sphinx-rtd-theme (1.2.0+dfsg-1) ... Selecting previously unselected package python3-msmb-theme. Preparing to unpack .../232-python3-msmb-theme_1.2.0-3_all.deb ... Unpacking python3-msmb-theme (1.2.0-3) ... Selecting previously unselected package python3-nbformat. Preparing to unpack .../233-python3-nbformat_5.5.0-1_all.deb ... Unpacking python3-nbformat (5.5.0-1) ... Selecting previously unselected package python3-nbclient. Preparing to unpack .../234-python3-nbclient_0.7.2-1_all.deb ... Unpacking python3-nbclient (0.7.2-1) ... Selecting previously unselected package python3-pandocfilters. Preparing to unpack .../235-python3-pandocfilters_1.5.0-1_all.deb ... Unpacking python3-pandocfilters (1.5.0-1) ... Selecting previously unselected package python3-tinycss2. Preparing to unpack .../236-python3-tinycss2_1.2.1-2_all.deb ... Unpacking python3-tinycss2 (1.2.1-2) ... Selecting previously unselected package python3-nbconvert. Preparing to unpack .../237-python3-nbconvert_6.5.3-3_all.deb ... Unpacking python3-nbconvert (6.5.3-3) ... Selecting previously unselected package python3-networkx. Preparing to unpack .../238-python3-networkx_2.8.8-1_all.deb ... Unpacking python3-networkx (2.8.8-1) ... Selecting previously unselected package python3-numexpr. Preparing to unpack .../239-python3-numexpr_2.8.4-1+b2_arm64.deb ... Unpacking python3-numexpr (2.8.4-1+b2) ... Selecting previously unselected package python3-numpydoc. Preparing to unpack .../240-python3-numpydoc_1.5.0-1_all.deb ... Unpacking python3-numpydoc (1.5.0-1) ... Selecting previously unselected package python3-pandas-lib:arm64. Preparing to unpack .../241-python3-pandas-lib_1.5.3+dfsg-2_arm64.deb ... Unpacking python3-pandas-lib:arm64 (1.5.3+dfsg-2) ... Selecting previously unselected package python3-pandas. Preparing to unpack .../242-python3-pandas_1.5.3+dfsg-2_all.deb ... Unpacking python3-pandas (1.5.3+dfsg-2) ... Selecting previously unselected package python3-threadpoolctl. Preparing to unpack .../243-python3-threadpoolctl_3.1.0-1_all.deb ... Unpacking python3-threadpoolctl (3.1.0-1) ... Selecting previously unselected package python3-sklearn-lib:arm64. Preparing to unpack .../244-python3-sklearn-lib_1.2.1+dfsg-1_arm64.deb ... Unpacking python3-sklearn-lib:arm64 (1.2.1+dfsg-1) ... Selecting previously unselected package python3-sklearn. Preparing to unpack .../245-python3-sklearn_1.2.1+dfsg-1_all.deb ... Unpacking python3-sklearn (1.2.1+dfsg-1) ... Selecting previously unselected package python3-tables-lib. Preparing to unpack .../246-python3-tables-lib_3.7.0-5+b1_arm64.deb ... Unpacking python3-tables-lib (3.7.0-5+b1) ... Selecting previously unselected package python3-tables. Preparing to unpack .../247-python3-tables_3.7.0-5_all.deb ... Unpacking python3-tables (3.7.0-5) ... Setting up media-types (10.0.0) ... Setting up libpipeline1:arm64 (1.5.7-1) ... Setting up libgraphite2-3:arm64 (1.3.14-1) ... Setting up liblcms2-2:arm64 (2.14-2) ... Setting up libxau6:arm64 (1:1.0.9-1) ... Setting up libpsl5:arm64 (0.21.2-1) ... Setting up libboost1.74-dev:arm64 (1.74.0+ds1-20) ... Setting up fonts-lato (2.0-2.1) ... Setting up fonts-mathjax (2.7.9+dfsg-1) ... Setting up libsodium23:arm64 (1.0.18-1) ... Setting up libicu72:arm64 (72.1-3) ... Setting up liblerc4:arm64 (4.0.0+ds-2) ... Setting up bsdextrautils (2.38.1-5+b1) ... Setting up libjs-mathjax (2.7.9+dfsg-1) ... Setting up libmagic-mgc (1:5.44-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libglib2.0-0:arm64 (2.74.6-1) ... No schema files found: doing nothing. Setting up libpgm-5.3-0:arm64 (5.3.128~dfsg-2) ... Setting up fonts-lyx (2.3.7-1) ... Setting up libdebhelper-perl (13.11.4) ... Setting up libbrotli1:arm64 (1.0.9-2+b6) ... Setting up libnorm1:arm64 (1.5.9+dfsg-2) ... Setting up x11-common (1:7.7+23) ... invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libnghttp2-14:arm64 (1.52.0-1) ... Setting up libmagic1:arm64 (1:5.44-3) ... Setting up libdeflate0:arm64 (1.14-1) ... Setting up gettext-base (0.21-12) ... Setting up m4 (1.4.19-3) ... Setting up libqhull-r8.0:arm64 (2020.2-5) ... Setting up liblzo2-2:arm64 (2.10-2) ... Setting up file (1:5.44-3) ... Setting up libjbig0:arm64 (2.1-6.1) ... Setting up libaec0:arm64 (1.0.6-1+b1) ... Setting up libsource-highlight-common (3.1.9-4.2) ... Setting up python-babel-localedata (2.10.3-1) ... Setting up libsnappy1v5:arm64 (1.1.9-3) ... Setting up libsasl2-modules-db:arm64 (2.1.28+dfsg-10) ... Setting up unicode-data (15.0.0-1) ... Setting up libxsimd-dev:arm64 (8.1.0-7) ... Setting up autotools-dev (20220109.1) ... Setting up libblas3:arm64 (3.11.0-2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode Setting up libexpat1-dev:arm64 (2.5.0-1) ... Setting up libjpeg62-turbo:arm64 (1:2.1.5-2) ... Setting up libx11-data (2:1.8.4-2) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libfribidi0:arm64 (1.0.8-2.1) ... Setting up libboost-regex1.74.0:arm64 (1.74.0+ds1-20) ... Setting up libimagequant0:arm64 (2.17.0-1) ... Setting up libproc2-0:arm64 (2:4.0.2-3) ... Setting up libpng16-16:arm64 (1.6.39-2) ... Setting up libtcl8.6:arm64 (8.6.13+dfsg-2) ... Setting up autopoint (0.21-12) ... Setting up fonts-dejavu-core (2.37-6) ... Setting up libsasl2-2:arm64 (2.1.28+dfsg-10) ... Setting up libgfortran5:arm64 (12.2.0-14) ... Setting up autoconf (2.71-3) ... Setting up libwebp7:arm64 (1.2.4-0.1) ... Setting up zlib1g-dev:arm64 (1:1.2.13.dfsg-1) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up libtiff6:arm64 (4.5.0-5) ... Setting up libuchardet0:arm64 (0.0.7-1) ... Setting up procps (2:4.0.2-3) ... Setting up python-tinycss2-common (1.2.1-2) ... Setting up libjson-perl (4.10000-1) ... Setting up libblosc1:arm64 (1.21.3+ds-1) ... Setting up libopenjp2-7:arm64 (2.5.0-1+b1) ... Setting up libsub-override-perl (0.09-4) ... Setting up libssh2-1:arm64 (1.10.0-3+b1) ... Setting up sgml-base (1.31) ... Setting up libboost-dev:arm64 (1.74.0.3) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up python-matplotlib-data (3.6.3-1) ... Setting up openssl (3.0.8-1) ... Setting up libwebpmux3:arm64 (1.2.4-0.1) ... Setting up libbsd0:arm64 (0.11.7-2) ... Setting up libelf1:arm64 (0.188-2.1) ... Setting up readline-common (8.2-1.3) ... Setting up libxml2:arm64 (2.9.14+dfsg-1.1+b3) ... Setting up python-tables-data (3.7.0-5) ... Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... Setting up sphinx-rtd-theme-common (1.2.0+dfsg-1) ... Setting up libsz2:arm64 (1.0.6-1+b1) ... Setting up libsource-highlight4v5:arm64 (3.1.9-4.2+b3) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up libdw1:arm64 (0.188-2.1) ... Setting up libxdmcp6:arm64 (1:1.1.2-3) ... Setting up liblapack3:arm64 (3.11.0-2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up libxcb1:arm64 (1.15-1) ... Setting up gettext (0.21-12) ... Setting up libopenblas0-pthread:arm64 (0.3.21+ds-4) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/openblas-pthread/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode update-alternatives: using /usr/lib/aarch64-linux-gnu/openblas-pthread/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode update-alternatives: using /usr/lib/aarch64-linux-gnu/openblas-pthread/libopenblas.so.0 to provide /usr/lib/aarch64-linux-gnu/libopenblas.so.0 (libopenblas.so.0-aarch64-linux-gnu) in auto mode Setting up libzmq5:arm64 (4.3.4-6) ... Setting up libtool (2.4.7-5) ... Setting up fontconfig-config (2.14.1-4) ... Setting up libwebpdemux2:arm64 (1.2.4-0.1) ... Setting up libreadline8:arm64 (8.2-1.3) ... Setting up libldap-2.5-0:arm64 (2.5.13+dfsg-5) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 140 added, 0 removed; done. Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libfreetype6:arm64 (2.12.1+dfsg-4) ... Setting up ucf (3.0043+nmu1) ... Setting up libbabeltrace1:arm64 (1.5.11-1+b2) ... Setting up libjs-sphinxdoc (5.3.0-4) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up libopenblas0:arm64 (0.3.21+ds-4) ... Setting up groff-base (1.22.4-10) ... Setting up xml-core (0.18+nmu1) ... Setting up libxslt1.1:arm64 (1.1.35-1) ... Setting up libcurl4:arm64 (7.88.1-8) ... Setting up libx11-6:arm64 (2:1.8.4-2) ... Setting up libharfbuzz0b:arm64 (6.0.0+dfsg-3) ... Setting up libfontconfig1:arm64 (2.14.1-4) ... Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1) ... Setting up libopenblas-pthread-dev:arm64 (0.3.21+ds-4) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/openblas-pthread/libblas.so to provide /usr/lib/aarch64-linux-gnu/libblas.so (libblas.so-aarch64-linux-gnu) in auto mode update-alternatives: using /usr/lib/aarch64-linux-gnu/openblas-pthread/liblapack.so to provide /usr/lib/aarch64-linux-gnu/liblapack.so (liblapack.so-aarch64-linux-gnu) in auto mode update-alternatives: using /usr/lib/aarch64-linux-gnu/openblas-pthread/libopenblas.so to provide /usr/lib/aarch64-linux-gnu/libopenblas.so (libopenblas.so-aarch64-linux-gnu) in auto mode Setting up libxrender1:arm64 (1:0.9.10-1.1) ... Setting up libdebuginfod-common (0.188-2.1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:arm64 (3.11.2-6) ... Setting up libxext6:arm64 (2:1.3.4-1+b1) ... Setting up libcurl3-gnutls:arm64 (7.88.1-8) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libopenblas-dev:arm64 (0.3.21+ds-4) ... Setting up libraqm0:arm64 (0.7.0-4.1) ... Setting up sphinx-common (5.3.0-4) ... Setting up libhdf5-103-1:arm64 (1.10.8+repack1-1) ... Setting up libxss1:arm64 (1:1.2.3-1) ... Setting up libpython3-stdlib:arm64 (3.11.2-1+b1) ... Setting up python3.11 (3.11.2-6) ... Setting up libxft2:arm64 (2.3.6-1) ... Setting up libpython3.11:arm64 (3.11.2-6) ... Setting up libtk8.6:arm64 (8.6.13-2) ... Setting up libdebuginfod1:arm64 (0.188-2.1) ... Setting up debhelper (13.11.4) ... Setting up python3 (3.11.2-1+b1) ... Setting up python3-pandocfilters (1.5.0-1) ... Setting up python3-markupsafe (2.1.2-1+b1) ... Setting up python3-webencodings (0.5.1-5) ... Setting up python3-psutil (5.9.4-1+b1) ... Setting up python3-tz (2022.7.1-3) ... Setting up python3-six (1.16.0-4) ... Setting up python3-roman (3.3-3) ... Setting up python3-decorator (5.1.1-3) ... Setting up python3-jinja2 (3.1.2-1) ... Setting up python3-packaging (23.0-1) ... Setting up gdb (13.1-2) ... Setting up python3-wcwidth (0.2.5+dfsg1-1.1) ... Setting up python3-pyparsing (3.0.9-1) ... Setting up python3-certifi (2022.9.24-1) ... Setting up python3-snowballstemmer (2.2.0-2) ... Setting up libpython3.11-dev:arm64 (3.11.2-6) ... Setting up python3-nest-asyncio (1.5.4-1) ... Setting up python3-brotli (1.0.9-2+b6) ... Setting up python3-cycler (0.11.0-1) ... Setting up python3-bytecode (0.14.0-2) ... Setting up python3-kiwisolver (1.4.4-1+b1) ... Setting up python3-idna (3.3-1) ... Setting up cython3 (0.29.32-2+b1) ... Setting up python3-html5lib (1.1-3) ... Setting up python3-pickleshare (0.7.5-5) ... Setting up python3-urllib3 (1.26.12-1) ... 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) ... Setting up python3-traitlets (5.5.0-1) ... Setting up python3-dateutil (2.8.2-2) ... Setting up python3-mpmath (1.2.1-2) ... Setting up python3-lib2to3 (3.11.2-2) ... Setting up python3-appdirs (1.4.4-3) ... Setting up python3-soupsieve (2.3.2-1) ... Setting up python3-cffi-backend:arm64 (1.15.1-5+b1) ... Setting up python3-imagesize (1.4.1-1) ... Setting up python3-ptyprocess (0.7.0-5) ... Setting up python3-pkg-resources (66.1.1-1) ... Setting up python3-entrypoints (0.4-2) ... Setting up python3-prompt-toolkit (3.0.36-2) ... Setting up python3-distutils (3.11.2-2) ... Setting up dh-python (5.20230130) ... Setting up python3-sympy (1.11.1-1) ... Setting up python3-attr (22.2.0-1) ... Setting up python3-tornado (6.2.0-3) ... Setting up python3-pure-eval (0.2.2-1) ... Setting up tk8.6-blt2.5 (2.5.3+dfsg-4.1) ... Setting up python3-astunparse (1.6.3-2) ... Setting up python3-tinycss2 (1.2.1-2) ... 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 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 > _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 > _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 > _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 > _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 > _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 > _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 > _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 > _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 building [mo]: targets for 0 po files that are out of date building [html]: targets for 29 source files that are out of date updating environment: [new config] 127 added, 0 changed, 0 removed reading sources... [ 0%] analysis reading sources... [ 1%] api/generated/mdtraj.Topology /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) reading sources... [ 2%] api/generated/mdtraj.Trajectory reading sources... [ 3%] api/generated/mdtraj.Trajectory.superpose reading sources... [ 3%] api/generated/mdtraj.acylindricity reading sources... [ 4%] api/generated/mdtraj.asphericity reading sources... [ 5%] api/generated/mdtraj.baker_hubbard reading sources... [ 6%] api/generated/mdtraj.chemical_shifts_ppm reading sources... [ 7%] api/generated/mdtraj.chemical_shifts_shiftx2 reading sources... [ 7%] api/generated/mdtraj.chemical_shifts_spartaplus reading sources... [ 8%] api/generated/mdtraj.compute_J3_HN_C reading sources... [ 9%] api/generated/mdtraj.compute_J3_HN_CB reading sources... [ 10%] api/generated/mdtraj.compute_J3_HN_HA reading sources... [ 11%] api/generated/mdtraj.compute_angles reading sources... [ 11%] api/generated/mdtraj.compute_center_of_mass reading sources... [ 12%] api/generated/mdtraj.compute_chi1 reading sources... [ 13%] api/generated/mdtraj.compute_chi2 reading sources... [ 14%] api/generated/mdtraj.compute_chi3 reading sources... [ 14%] api/generated/mdtraj.compute_chi4 reading sources... [ 15%] api/generated/mdtraj.compute_contacts reading sources... [ 16%] api/generated/mdtraj.compute_dihedrals reading sources... [ 17%] api/generated/mdtraj.compute_directors reading sources... [ 18%] api/generated/mdtraj.compute_displacements reading sources... [ 18%] api/generated/mdtraj.compute_distances reading sources... [ 19%] api/generated/mdtraj.compute_drid reading sources... [ 20%] api/generated/mdtraj.compute_dssp reading sources... [ 21%] api/generated/mdtraj.compute_gyration_tensor reading sources... [ 22%] api/generated/mdtraj.compute_inertia_tensor reading sources... [ 22%] api/generated/mdtraj.compute_neighbors reading sources... [ 23%] api/generated/mdtraj.compute_nematic_order reading sources... [ 24%] api/generated/mdtraj.compute_omega reading sources... [ 25%] api/generated/mdtraj.compute_phi reading sources... [ 25%] api/generated/mdtraj.compute_psi reading sources... [ 26%] api/generated/mdtraj.compute_rdf reading sources... [ 27%] api/generated/mdtraj.compute_rg reading sources... [ 28%] api/generated/mdtraj.density reading sources... [ 29%] api/generated/mdtraj.dipole_moments reading sources... [ 29%] api/generated/mdtraj.formats.AmberNetCDFRestartFile reading sources... [ 30%] api/generated/mdtraj.formats.AmberRestartFile reading sources... [ 31%] api/generated/mdtraj.formats.ArcTrajectoryFile reading sources... [ 32%] api/generated/mdtraj.formats.BINPOSTrajectoryFile reading sources... [ 33%] api/generated/mdtraj.formats.DCDTrajectoryFile reading sources... [ 33%] api/generated/mdtraj.formats.DTRTrajectoryFile reading sources... [ 34%] api/generated/mdtraj.formats.GroTrajectoryFile reading sources... [ 35%] api/generated/mdtraj.formats.HDF5TrajectoryFile reading sources... [ 36%] api/generated/mdtraj.formats.LAMMPSTrajectoryFile reading sources... [ 37%] api/generated/mdtraj.formats.LH5TrajectoryFile reading sources... [ 37%] api/generated/mdtraj.formats.MDCRDTrajectoryFile reading sources... [ 38%] api/generated/mdtraj.formats.NetCDFTrajectoryFile reading sources... [ 39%] api/generated/mdtraj.formats.PDBTrajectoryFile reading sources... [ 40%] api/generated/mdtraj.formats.TRRTrajectoryFile reading sources... [ 40%] api/generated/mdtraj.formats.XTCTrajectoryFile reading sources... [ 41%] api/generated/mdtraj.formats.XYZTrajectoryFile reading sources... [ 42%] api/generated/mdtraj.geometry.squareform reading sources... [ 43%] api/generated/mdtraj.isothermal_compressability_kappa_T reading sources... [ 44%] api/generated/mdtraj.iterload reading sources... [ 44%] api/generated/mdtraj.join reading sources... [ 45%] api/generated/mdtraj.kabsch_sander reading sources... [ 46%] api/generated/mdtraj.load reading sources... [ 47%] api/generated/mdtraj.load_arc reading sources... [ 48%] api/generated/mdtraj.load_binpos reading sources... [ 48%] api/generated/mdtraj.load_dcd reading sources... [ 49%] api/generated/mdtraj.load_dtr reading sources... [ 50%] api/generated/mdtraj.load_frame reading sources... [ 51%] api/generated/mdtraj.load_hdf5 reading sources... [ 51%] api/generated/mdtraj.load_hoomdxml reading sources... [ 52%] api/generated/mdtraj.load_lammpstrj reading sources... [ 53%] api/generated/mdtraj.load_lh5 reading sources... [ 54%] api/generated/mdtraj.load_netcdf reading sources... [ 55%] api/generated/mdtraj.load_pdb reading sources... [ 55%] api/generated/mdtraj.load_prmtop reading sources... [ 56%] api/generated/mdtraj.load_trr reading sources... [ 57%] api/generated/mdtraj.load_xml reading sources... [ 58%] api/generated/mdtraj.load_xtc reading sources... [ 59%] api/generated/mdtraj.load_xyz reading sources... [ 59%] api/generated/mdtraj.lprmsd reading sources... [ 60%] api/generated/mdtraj.open reading sources... [ 61%] api/generated/mdtraj.principal_moments reading sources... [ 62%] api/generated/mdtraj.reindex_dataframe_by_atoms reading sources... [ 62%] api/generated/mdtraj.relative_shape_antisotropy reading sources... [ 63%] api/generated/mdtraj.reporters.DCDReporter reading sources... [ 64%] api/generated/mdtraj.reporters.HDF5Reporter reading sources... [ 65%] api/generated/mdtraj.reporters.NetCDFReporter reading sources... [ 66%] api/generated/mdtraj.rmsd reading sources... [ 66%] api/generated/mdtraj.rmsf reading sources... [ 67%] api/generated/mdtraj.shrake_rupley reading sources... [ 68%] api/generated/mdtraj.static_dielectric reading sources... [ 69%] api/generated/mdtraj.thermal_expansion_alpha_P reading sources... [ 70%] api/generated/mdtraj.utils.box_vectors_to_lengths_and_angles reading sources... [ 70%] api/generated/mdtraj.utils.check_random_state reading sources... [ 71%] api/generated/mdtraj.utils.ensure_type reading sources... [ 72%] api/generated/mdtraj.utils.ilen reading sources... [ 73%] api/generated/mdtraj.utils.import_ reading sources... [ 74%] api/generated/mdtraj.utils.in_units_of reading sources... [ 74%] api/generated/mdtraj.utils.lengths_and_angles_to_box_vectors reading sources... [ 75%] api/generated/mdtraj.utils.rotation_matrix_from_quaternion reading sources... [ 76%] api/generated/mdtraj.utils.timing reading sources... [ 77%] api/generated/mdtraj.utils.uniform_quaternion reading sources... [ 77%] api/generated/mdtraj.wernet_nilsson reading sources... [ 78%] api/reporters reading sources... [ 79%] api/trajectory_files reading sources... [ 80%] api/utils reading sources... [ 81%] atom_selection reading sources... [ 81%] building_docs reading sources... [ 82%] examples/atom-selection reading sources... [ 83%] examples/centroids reading sources... [ 84%] examples/clustering reading sources... [ 85%] examples/hbonds reading sources... [ 85%] examples/index reading sources... [ 86%] examples/introduction reading sources... [ 87%] examples/iterload reading sources... [ 88%] examples/native-contact reading sources... [ 88%] examples/nmr reading sources... [ 89%] examples/openmm reading sources... [ 90%] examples/pca reading sources... [ 91%] examples/ramachandran-plot reading sources... [ 92%] examples/rmsd-benchmark reading sources... [ 92%] examples/solvent-accessible-surface-area reading sources... [ 93%] examples/two-pass-clustering reading sources... [ 94%] faq reading sources... [ 95%] hdf5_format reading sources... [ 96%] index reading sources... [ 96%] installation reading sources... [ 97%] load_functions reading sources... [ 98%] mdconvert reading sources... [ 99%] new_to_python reading sources... [100%] whatsnew /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: /build/mdtraj-1.9.7/docs/examples/centroids.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/centroids.ipynb :skip_exceptions: /build/mdtraj-1.9.7/docs/examples/clustering.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/clustering.ipynb :skip_exceptions: /build/mdtraj-1.9.7/docs/examples/hbonds.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/hbonds.ipynb :skip_exceptions: /build/mdtraj-1.9.7/docs/examples/iterload.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/iterload.ipynb :skip_exceptions: /build/mdtraj-1.9.7/docs/examples/native-contact.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/native-contact.ipynb :skip_exceptions: /build/mdtraj-1.9.7/docs/examples/nmr.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/nmr.ipynb :skip_exceptions: /build/mdtraj-1.9.7/docs/examples/openmm.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/simulation-with-openmm.ipynb :skip_exceptions: /build/mdtraj-1.9.7/docs/examples/pca.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/principal-components.ipynb :skip_exceptions: /build/mdtraj-1.9.7/docs/examples/ramachandran-plot.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/ramachandran-plot.ipynb :skip_exceptions: /build/mdtraj-1.9.7/docs/examples/rmsd-benchmark.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/rmsd-benchmark.ipynb :skip_exceptions: /build/mdtraj-1.9.7/docs/examples/solvent-accessible-surface-area.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/solvent-accessible-surface-area.ipynb :skip_exceptions: /build/mdtraj-1.9.7/docs/examples/two-pass-clustering.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/two-pass-clustering.ipynb :skip_exceptions: /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 pickling environment... done checking consistency... /build/mdtraj-1.9.7/docs/building_docs.rst: WARNING: document isn't included in any toctree /build/mdtraj-1.9.7/docs/faq.rst: WARNING: document isn't included in any toctree done preparing documents... done writing output... [ 0%] analysis writing output... [ 1%] api/generated/mdtraj.Topology writing output... [ 2%] api/generated/mdtraj.Trajectory writing output... [ 3%] api/generated/mdtraj.Trajectory.superpose writing output... [ 3%] api/generated/mdtraj.acylindricity writing output... [ 4%] api/generated/mdtraj.asphericity writing output... [ 5%] api/generated/mdtraj.baker_hubbard writing output... [ 6%] api/generated/mdtraj.chemical_shifts_ppm writing output... [ 7%] api/generated/mdtraj.chemical_shifts_shiftx2 writing output... [ 7%] api/generated/mdtraj.chemical_shifts_spartaplus writing output... [ 8%] api/generated/mdtraj.compute_J3_HN_C writing output... [ 9%] api/generated/mdtraj.compute_J3_HN_CB writing output... [ 10%] api/generated/mdtraj.compute_J3_HN_HA writing output... [ 11%] api/generated/mdtraj.compute_angles writing output... [ 11%] api/generated/mdtraj.compute_center_of_mass writing output... [ 12%] api/generated/mdtraj.compute_chi1 writing output... [ 13%] api/generated/mdtraj.compute_chi2 writing output... [ 14%] api/generated/mdtraj.compute_chi3 writing output... [ 14%] api/generated/mdtraj.compute_chi4 writing output... [ 15%] api/generated/mdtraj.compute_contacts writing output... [ 16%] api/generated/mdtraj.compute_dihedrals writing output... [ 17%] api/generated/mdtraj.compute_directors writing output... [ 18%] api/generated/mdtraj.compute_displacements writing output... [ 18%] api/generated/mdtraj.compute_distances writing output... [ 19%] api/generated/mdtraj.compute_drid writing output... [ 20%] api/generated/mdtraj.compute_dssp writing output... [ 21%] api/generated/mdtraj.compute_gyration_tensor writing output... [ 22%] api/generated/mdtraj.compute_inertia_tensor writing output... [ 22%] api/generated/mdtraj.compute_neighbors writing output... [ 23%] api/generated/mdtraj.compute_nematic_order writing output... [ 24%] api/generated/mdtraj.compute_omega writing output... [ 25%] api/generated/mdtraj.compute_phi writing output... [ 25%] api/generated/mdtraj.compute_psi writing output... [ 26%] api/generated/mdtraj.compute_rdf writing output... [ 27%] api/generated/mdtraj.compute_rg writing output... [ 28%] api/generated/mdtraj.density writing output... [ 29%] api/generated/mdtraj.dipole_moments writing output... [ 29%] api/generated/mdtraj.formats.AmberNetCDFRestartFile writing output... [ 30%] api/generated/mdtraj.formats.AmberRestartFile writing output... [ 31%] api/generated/mdtraj.formats.ArcTrajectoryFile writing output... [ 32%] api/generated/mdtraj.formats.BINPOSTrajectoryFile writing output... [ 33%] api/generated/mdtraj.formats.DCDTrajectoryFile writing output... [ 33%] api/generated/mdtraj.formats.DTRTrajectoryFile writing output... [ 34%] api/generated/mdtraj.formats.GroTrajectoryFile writing output... [ 35%] api/generated/mdtraj.formats.HDF5TrajectoryFile writing output... [ 36%] api/generated/mdtraj.formats.LAMMPSTrajectoryFile writing output... [ 37%] api/generated/mdtraj.formats.LH5TrajectoryFile writing output... [ 37%] api/generated/mdtraj.formats.MDCRDTrajectoryFile writing output... [ 38%] api/generated/mdtraj.formats.NetCDFTrajectoryFile writing output... [ 39%] api/generated/mdtraj.formats.PDBTrajectoryFile writing output... [ 40%] api/generated/mdtraj.formats.TRRTrajectoryFile writing output... [ 40%] api/generated/mdtraj.formats.XTCTrajectoryFile writing output... [ 41%] api/generated/mdtraj.formats.XYZTrajectoryFile writing output... [ 42%] api/generated/mdtraj.geometry.squareform writing output... [ 43%] api/generated/mdtraj.isothermal_compressability_kappa_T writing output... [ 44%] api/generated/mdtraj.iterload writing output... [ 44%] api/generated/mdtraj.join writing output... [ 45%] api/generated/mdtraj.kabsch_sander writing output... [ 46%] api/generated/mdtraj.load writing output... [ 47%] api/generated/mdtraj.load_arc writing output... [ 48%] api/generated/mdtraj.load_binpos writing output... [ 48%] api/generated/mdtraj.load_dcd writing output... [ 49%] api/generated/mdtraj.load_dtr writing output... [ 50%] api/generated/mdtraj.load_frame writing output... [ 51%] api/generated/mdtraj.load_hdf5 writing output... [ 51%] api/generated/mdtraj.load_hoomdxml writing output... [ 52%] api/generated/mdtraj.load_lammpstrj writing output... [ 53%] api/generated/mdtraj.load_lh5 writing output... [ 54%] api/generated/mdtraj.load_netcdf writing output... [ 55%] api/generated/mdtraj.load_pdb writing output... [ 55%] api/generated/mdtraj.load_prmtop writing output... [ 56%] api/generated/mdtraj.load_trr writing output... [ 57%] api/generated/mdtraj.load_xml writing output... [ 58%] api/generated/mdtraj.load_xtc writing output... [ 59%] api/generated/mdtraj.load_xyz writing output... [ 59%] api/generated/mdtraj.lprmsd writing output... [ 60%] api/generated/mdtraj.open writing output... [ 61%] api/generated/mdtraj.principal_moments writing output... [ 62%] api/generated/mdtraj.reindex_dataframe_by_atoms writing output... [ 62%] api/generated/mdtraj.relative_shape_antisotropy writing output... [ 63%] api/generated/mdtraj.reporters.DCDReporter writing output... [ 64%] api/generated/mdtraj.reporters.HDF5Reporter writing output... [ 65%] api/generated/mdtraj.reporters.NetCDFReporter writing output... [ 66%] api/generated/mdtraj.rmsd writing output... [ 66%] api/generated/mdtraj.rmsf writing output... [ 67%] api/generated/mdtraj.shrake_rupley writing output... [ 68%] api/generated/mdtraj.static_dielectric writing output... [ 69%] api/generated/mdtraj.thermal_expansion_alpha_P writing output... [ 70%] api/generated/mdtraj.utils.box_vectors_to_lengths_and_angles writing output... [ 70%] api/generated/mdtraj.utils.check_random_state writing output... [ 71%] api/generated/mdtraj.utils.ensure_type writing output... [ 72%] api/generated/mdtraj.utils.ilen writing output... [ 73%] api/generated/mdtraj.utils.import_ writing output... [ 74%] api/generated/mdtraj.utils.in_units_of writing output... [ 74%] api/generated/mdtraj.utils.lengths_and_angles_to_box_vectors writing output... [ 75%] api/generated/mdtraj.utils.rotation_matrix_from_quaternion writing output... [ 76%] api/generated/mdtraj.utils.timing writing output... [ 77%] api/generated/mdtraj.utils.uniform_quaternion writing output... [ 77%] api/generated/mdtraj.wernet_nilsson writing output... [ 78%] api/reporters writing output... [ 79%] api/trajectory_files writing output... [ 80%] api/utils writing output... [ 81%] atom_selection writing output... [ 81%] building_docs writing output... [ 82%] examples/atom-selection writing output... [ 83%] examples/centroids writing output... [ 84%] examples/clustering writing output... [ 85%] examples/hbonds writing output... [ 85%] examples/index writing output... [ 86%] examples/introduction writing output... [ 87%] examples/iterload writing output... [ 88%] examples/native-contact writing output... [ 88%] examples/nmr writing output... [ 89%] examples/openmm writing output... [ 90%] examples/pca writing output... [ 91%] examples/ramachandran-plot writing output... [ 92%] examples/rmsd-benchmark writing output... [ 92%] examples/solvent-accessible-surface-area writing output... [ 93%] examples/two-pass-clustering writing output... [ 94%] faq writing output... [ 95%] hdf5_format writing output... [ 96%] index writing output... [ 96%] installation writing output... [ 97%] load_functions writing output... [ 98%] mdconvert writing output... [ 99%] new_to_python writing output... [100%] whatsnew 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 > _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 > _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 > _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 > _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 > _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 > _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 > _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 > _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 > _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 > _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 > _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 > _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 > _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 > _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 > _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 > _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 Changed-By: Drew Parsons 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'