I: pbuilder: network access will be disabled during build I: Current time: Tue Dec 16 03:36:02 +14 2025 I: pbuilder-time-stamp: 1765805762 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [mdtraj_1.10.1-2.dsc] I: copying [./mdtraj_1.10.1.orig.tar.gz] I: copying [./mdtraj_1.10.1-2.debian.tar.xz] I: Extracting source gpgv: Signature made Mon Nov 11 19:58:43 2024 gpgv: using RSA key 13796755BBC72BB8ABE2AEB5FA9DEC5DE11C63F1 gpgv: issuer "eamanu@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./mdtraj_1.10.1-2.dsc: no acceptable signature found dpkg-source: info: extracting mdtraj in mdtraj-1.10.1 dpkg-source: info: unpacking mdtraj_1.10.1.orig.tar.gz dpkg-source: info: unpacking mdtraj_1.10.1-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying docs_use_local_mathjax.patch dpkg-source: info: applying build_dir_pybuild.patch dpkg-source: info: applying python_hashbang.patch dpkg-source: info: applying 32bit_skip_image_molecule.patch dpkg-source: info: applying test_relax_tol.patch dpkg-source: info: applying rename-mdconvert-mdtraj.patch dpkg-source: info: applying drop_notebook_in_docs.patch dpkg-source: info: applying test_increase_timeout.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2563990/tmp/hooks/D01_modify_environment starting debug: Running on codethink01-arm64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Dec 15 13:36 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/2563990/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/2563990/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="32" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") BASH_VERSION='5.2.32(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=arm64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DIRSTACK=() DISTRIBUTION=unstable EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' INVOCATION_ID=8c839db2cc394578b9784ba652d38001 LANG=C LANGUAGE=nl_BE:nl LC_ALL=C MACHTYPE=aarch64-unknown-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=2563990 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.8J28rdBb/pbuilderrc_nZf2 --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.8J28rdBb/b2 --logfile b2/build.log mdtraj_1.10.1-2.dsc' SUDO_GID=109 SUDO_UID=104 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://192.168.101.4:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-27-cloud-arm64 #1 SMP Debian 6.1.115-1 (2024-11-01) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2563990/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-sequence-python3, cython3, pandoc, python3-setuptools, python3-all-dev, python3-gsd, python3-numpy, python3-scipy, python3-nbsphinx, python3-nbsphinx-link, python3-netcdf4, python3-networkx, python3-pandas, python3-pyparsing, python3-sphinx, python3-tables, python3-versioneer, libjs-mathjax, python3-msmb-theme, python3-ipykernel, python3-jupyter-client, python3-matplotlib, python3-nbconvert, python3-nbformat, python3-numpydoc, python3-sklearn dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 20088 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-sequence-python3; however: Package dh-sequence-python3 is not installed. pbuilder-satisfydepends-dummy depends on cython3; however: Package cython3 is not installed. pbuilder-satisfydepends-dummy depends on pandoc; however: Package pandoc is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-all-dev; however: Package python3-all-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-gsd; however: Package python3-gsd is not installed. pbuilder-satisfydepends-dummy depends on python3-numpy; however: Package python3-numpy is not installed. pbuilder-satisfydepends-dummy depends on python3-scipy; however: Package python3-scipy is not installed. pbuilder-satisfydepends-dummy depends on python3-nbsphinx; however: Package python3-nbsphinx is not installed. pbuilder-satisfydepends-dummy depends on python3-nbsphinx-link; however: Package python3-nbsphinx-link is not installed. pbuilder-satisfydepends-dummy depends on python3-netcdf4; however: Package python3-netcdf4 is not installed. pbuilder-satisfydepends-dummy depends on python3-networkx; however: Package python3-networkx is not installed. pbuilder-satisfydepends-dummy depends on python3-pandas; however: Package python3-pandas is not installed. pbuilder-satisfydepends-dummy depends on python3-pyparsing; however: Package python3-pyparsing is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx; however: Package python3-sphinx is not installed. pbuilder-satisfydepends-dummy depends on python3-tables; however: Package python3-tables is not installed. pbuilder-satisfydepends-dummy depends on python3-versioneer; however: Package python3-versioneer is not installed. pbuilder-satisfydepends-dummy depends on libjs-mathjax; however: Package libjs-mathjax is not installed. pbuilder-satisfydepends-dummy depends on python3-msmb-theme; however: Package python3-msmb-theme is not installed. pbuilder-satisfydepends-dummy depends on python3-ipykernel; however: Package python3-ipykernel is not installed. pbuilder-satisfydepends-dummy depends on python3-jupyter-client; however: Package python3-jupyter-client is not installed. pbuilder-satisfydepends-dummy depends on python3-matplotlib; however: Package python3-matplotlib is not installed. pbuilder-satisfydepends-dummy depends on python3-nbconvert; however: Package python3-nbconvert is not installed. pbuilder-satisfydepends-dummy depends on python3-nbformat; however: Package python3-nbformat is not installed. pbuilder-satisfydepends-dummy depends on python3-numpydoc; however: Package python3-numpydoc is not installed. pbuilder-satisfydepends-dummy depends on python3-sklearn; however: Package python3-sklearn is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} blt{a} bsdextrautils{a} ca-certificates{a} cython3{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} docutils-common{a} dwz{a} file{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} fonts-font-awesome{a} fonts-lato{a} fonts-lyx{a} fonts-mathjax{a} gdb{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libaec0{a} libarchive-zip-perl{a} libbabeltrace1{a} libblas3{a} libblosc1{a} libblosc2-4{a} libbrotli1{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4t64{a} libdebhelper-perl{a} libdebuginfod-common{a} libdebuginfod1t64{a} libdeflate0{a} libdw1t64{a} libelf1t64{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgfortran5{a} libglib2.0-0t64{a} libgraphite2-3{a} libgssapi-krb5-2{a} libharfbuzz0b{a} libhdf5-103-1t64{a} libhdf5-hl-100t64{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-c5{a} libjson-perl{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} liblbfgsb0{a} liblcms2-2{a} libldap-2.5-0{a} liblerc4{a} liblua5.4-0{a} liblzo2-2{a} libmagic-mgc{a} libmagic1t64{a} libnetcdf19t64{a} libnghttp2-14{a} libnghttp3-9{a} libngtcp2-16{a} libngtcp2-crypto-gnutls8{a} libnorm1t64{a} libnsl2{a} libnuma1{a} libopenjp2-7{a} libpgm-5.3-0t64{a} libpipeline1{a} libpng16-16t64{a} libproc2-0{a} libpsl5t64{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.12-dev{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libpython3.12t64{a} libqhull-r8.0{a} libraqm0{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsharpyuv0{a} libsnappy1v5{a} libsodium23{a} libsource-highlight-common{a} libsource-highlight4t64{a} libssh2-1t64{a} libsz2{a} libtcl8.6{a} libtiff6{a} libtirpc-common{a} libtirpc3t64{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} libxslt1.1{a} libxss1{a} libyaml-0-2{a} libzmq5{a} m4{a} man-db{a} media-types{a} netbase{a} openssl{a} pandoc{a} pandoc-data{a} po-debconf{a} procps{a} python-babel-localedata{a} python-matplotlib-data{a} python-tables-data{a} python-tinycss2-common{a} python3{a} python3-alabaster{a} python3-all{a} python3-all-dev{a} python3-appdirs{a} python3-asttokens{a} python3-attr{a} python3-autocommand{a} python3-babel{a} python3-bleach{a} python3-brotli{a} python3-bs4{a} python3-certifi{a} python3-cffi-backend{a} python3-cftime{a} python3-chardet{a} python3-charset-normalizer{a} python3-comm{a} python3-contourpy{a} python3-coverage{a} python3-cpuinfo{a} python3-cycler{a} python3-dateutil{a} python3-debugpy{a} python3-decorator{a} python3-defusedxml{a} python3-dev{a} python3-docutils{a} python3-executing{a} python3-fastjsonschema{a} python3-fonttools{a} python3-fs{a} python3-gsd{a} python3-html5lib{a} python3-idna{a} python3-imagesize{a} python3-inflect{a} python3-ipykernel{a} python3-ipython{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-jedi{a} python3-jinja2{a} python3-joblib{a} python3-jsonschema{a} python3-jsonschema-specifications{a} python3-jupyter-client{a} python3-jupyter-core{a} python3-jupyterlab-pygments{a} python3-kiwisolver{a} python3-lxml{a} python3-lz4{a} python3-markupsafe{a} python3-matplotlib{a} python3-matplotlib-inline{a} python3-minimal{a} python3-mistune{a} python3-more-itertools{a} python3-mpmath{a} python3-msmb-theme{a} python3-nbclient{a} python3-nbconvert{a} python3-nbformat{a} python3-nbsphinx{a} python3-nbsphinx-link{a} python3-nest-asyncio{a} python3-netcdf4{a} python3-networkx{a} python3-numexpr{a} python3-numpy{a} python3-numpydoc{a} python3-packaging{a} python3-pandas{a} python3-pandas-lib{a} python3-pandocfilters{a} python3-parso{a} python3-pexpect{a} python3-pil{a} python3-pil.imagetk{a} python3-pkg-resources{a} python3-platformdirs{a} python3-prompt-toolkit{a} python3-psutil{a} python3-ptyprocess{a} python3-pure-eval{a} python3-py{a} python3-pygments{a} python3-pyparsing{a} python3-referencing{a} python3-requests{a} python3-roman{a} python3-rpds-py{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-sphinxcontrib.jquery{a} python3-stack-data{a} python3-sympy{a} python3-tables{a} python3-tables-lib{a} python3-tabulate{a} python3-threadpoolctl{a} python3-tinycss2{a} python3-tk{a} python3-tornado{a} python3-traitlets{a} python3-typeguard{a} python3-typeshed{a} python3-typing-extensions{a} python3-tz{a} python3-ufolib2{a} python3-urllib3{a} python3-versioneer{a} python3-wcwidth{a} python3-webencodings{a} python3-zipp{a} python3-zmq{a} python3.12{a} python3.12-dev{a} python3.12-minimal{a} python3.12-tk{a} python3.13-tk{a} readline-common{a} sensible-utils{a} sgml-base{a} sphinx-common{a} sphinx-rtd-theme-common{a} tk8.6-blt2.5{a} tzdata{a} ucf{a} unicode-data{a} x11-common{a} xml-core{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl isympy-common javascript-common krb5-locales libarchive-cpio-perl libc6-dbg libglib2.0-data libjson-xs-perl libldap-common libltdl-dev libmail-sendmail-perl libpaper-utils libsasl2-modules linux-sysctl-defaults lynx psmisc publicsuffix python3-bottleneck python3-cssselect python3-gdal python3-json-pointer python3-odf python3-olefile python3-openpyxl python3-pydot python3-pygraphviz python3-pytest python3-rfc3987 python3-simplejson python3-sphinxcontrib.bibtex python3-uritemplate python3-webcolors python3-yaml shared-mime-info wget xdg-user-dirs 0 packages upgraded, 291 newly installed, 0 to remove and 0 not upgraded. Need to get 192 MB of archives. After unpacking 983 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 fonts-lato all 2.015-1 [2780 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 ucf all 3.0043+nmu1 [55.2 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 libdebuginfod-common all 0.192-4 [23.7 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 libpython3.12-minimal arm64 3.12.7-3 [808 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 libexpat1 arm64 2.6.4-1 [90.7 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 python3.12-minimal arm64 3.12.7-3 [1940 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 python3-minimal arm64 3.12.6-1 [26.7 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 media-types all 10.1.0 [26.9 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 netbase all 6.4 [12.8 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 tzdata all 2024b-3 [255 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 libkrb5support0 arm64 1.21.3-3 [32.1 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 libcom-err2 arm64 1.47.1-1+b1 [23.1 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 libk5crypto3 arm64 1.21.3-3 [80.8 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 libkeyutils1 arm64 1.6.3-4 [9352 B] Get: 16 http://deb.debian.org/debian unstable/main arm64 libkrb5-3 arm64 1.21.3-3 [310 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 libgssapi-krb5-2 arm64 1.21.3-3 [126 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 libtirpc3t64 arm64 1.3.4+ds-1.3+b1 [78.7 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 libnsl2 arm64 1.3.0-3+b3 [37.9 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 readline-common all 8.2-5 [69.3 kB] Get: 22 http://deb.debian.org/debian unstable/main arm64 libreadline8t64 arm64 8.2-5 [159 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 libpython3.12-stdlib arm64 3.12.7-3 [1902 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 python3.12 arm64 3.12.7-3 [671 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 libpython3-stdlib arm64 3.12.6-1 [9692 B] Get: 26 http://deb.debian.org/debian unstable/main arm64 python3 arm64 3.12.6-1 [27.8 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 sgml-base all 1.31 [15.4 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 libproc2-0 arm64 2:4.0.4-6 [62.3 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 procps arm64 2:4.0.4-6 [872 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 openssl arm64 3.3.2-2 [1347 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 ca-certificates all 20240203 [158 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.22.5-2 [198 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-5 [1129 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40.2-10 [96.5 kB] Get: 39 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 40 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 41 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 42 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3 [493 kB] Get: 43 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 44 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 45 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.22.5-2 [723 kB] Get: 46 http://deb.debian.org/debian unstable/main arm64 libtcl8.6 arm64 8.6.15+dfsg-2 [982 kB] Get: 47 http://deb.debian.org/debian unstable/main arm64 libbrotli1 arm64 1.1.0-2+b5 [296 kB] Get: 48 http://deb.debian.org/debian unstable/main arm64 libpng16-16t64 arm64 1.6.44-2 [273 kB] Get: 49 http://deb.debian.org/debian unstable/main arm64 libfreetype6 arm64 2.13.3+dfsg-1 [422 kB] Get: 50 http://deb.debian.org/debian unstable/main arm64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 51 http://deb.debian.org/debian unstable/main arm64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 52 http://deb.debian.org/debian unstable/main arm64 fontconfig-config arm64 2.15.0-1.1+b1 [318 kB] Get: 53 http://deb.debian.org/debian unstable/main arm64 libfontconfig1 arm64 2.15.0-1.1+b1 [387 kB] Get: 54 http://deb.debian.org/debian unstable/main arm64 libxau6 arm64 1:1.0.11-1 [20.6 kB] Get: 55 http://deb.debian.org/debian unstable/main arm64 libxdmcp6 arm64 1:1.1.2-3+b2 [24.4 kB] Get: 56 http://deb.debian.org/debian unstable/main arm64 libxcb1 arm64 1.17.0-2+b1 [143 kB] Get: 57 http://deb.debian.org/debian unstable/main arm64 libx11-data all 2:1.8.10-2 [337 kB] Get: 58 http://deb.debian.org/debian unstable/main arm64 libx11-6 arm64 2:1.8.10-2 [789 kB] Get: 59 http://deb.debian.org/debian unstable/main arm64 libxrender1 arm64 1:0.9.10-1.1+b2 [27.2 kB] Get: 60 http://deb.debian.org/debian unstable/main arm64 libxft2 arm64 2.3.6-1+b2 [51.6 kB] Get: 61 http://deb.debian.org/debian unstable/main arm64 libxext6 arm64 2:1.3.4-1+b2 [49.3 kB] Get: 62 http://deb.debian.org/debian unstable/main arm64 x11-common all 1:7.7+23.1 [216 kB] Get: 63 http://deb.debian.org/debian unstable/main arm64 libxss1 arm64 1:1.2.3-1+b2 [17.1 kB] Get: 64 http://deb.debian.org/debian unstable/main arm64 libtk8.6 arm64 8.6.15-1 [738 kB] Get: 65 http://deb.debian.org/debian unstable/main arm64 tk8.6-blt2.5 arm64 2.5.3+dfsg-7+b1 [538 kB] Get: 66 http://deb.debian.org/debian unstable/main arm64 blt arm64 2.5.3+dfsg-7+b1 [6344 B] Get: 67 http://deb.debian.org/debian unstable/main arm64 cython3 arm64 3.0.11+dfsg-1 [2192 kB] Get: 68 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.20 [89.7 kB] Get: 69 http://deb.debian.org/debian unstable/main arm64 libtool all 2.4.7-8 [517 kB] Get: 70 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 71 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 72 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 73 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 74 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 75 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 76 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-5+b1 [9239 kB] Get: 77 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2 [630 kB] Get: 78 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.22.5-2 [1532 kB] Get: 79 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 80 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 81 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.20 [915 kB] Get: 82 http://deb.debian.org/debian unstable/main arm64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 83 http://deb.debian.org/debian unstable/main arm64 python3-more-itertools all 10.5.0-1 [63.8 kB] Get: 84 http://deb.debian.org/debian unstable/main arm64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 85 http://deb.debian.org/debian unstable/main arm64 python3-typeguard all 4.4.1-1 [37.0 kB] Get: 86 http://deb.debian.org/debian unstable/main arm64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 87 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 88 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 89 http://deb.debian.org/debian unstable/main arm64 python3-pkg-resources all 75.2.0-1 [213 kB] Get: 90 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 91 http://deb.debian.org/debian unstable/main arm64 python3-zipp all 3.21.0-1 [10.6 kB] Get: 92 http://deb.debian.org/debian unstable/main arm64 python3-setuptools all 75.2.0-1 [731 kB] Get: 93 http://deb.debian.org/debian unstable/main arm64 dh-python all 6.20241024 [109 kB] Get: 94 http://deb.debian.org/debian unstable/main arm64 xml-core all 0.19 [20.1 kB] Get: 95 http://deb.debian.org/debian unstable/main arm64 docutils-common all 0.21.2+dfsg-2 [128 kB] Get: 96 http://deb.debian.org/debian unstable/main arm64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [517 kB] Get: 97 http://deb.debian.org/debian unstable/main arm64 fonts-lyx all 2.4.2.1-1 [190 kB] Get: 98 http://deb.debian.org/debian unstable/main arm64 fonts-mathjax all 2.7.9+dfsg-1 [2210 kB] Get: 99 http://deb.debian.org/debian unstable/main arm64 libdw1t64 arm64 0.192-4 [237 kB] Get: 100 http://deb.debian.org/debian unstable/main arm64 libglib2.0-0t64 arm64 2.82.2-2 [1409 kB] Get: 101 http://deb.debian.org/debian unstable/main arm64 libbabeltrace1 arm64 1.5.11-4 [163 kB] Get: 102 http://deb.debian.org/debian unstable/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-8 [20.0 kB] Get: 103 http://deb.debian.org/debian unstable/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-8 [55.4 kB] Get: 104 http://deb.debian.org/debian unstable/main arm64 libldap-2.5-0 arm64 2.5.18+dfsg-3+b1 [175 kB] Get: 105 http://deb.debian.org/debian unstable/main arm64 libnghttp2-14 arm64 1.64.0-1 [71.3 kB] Get: 106 http://deb.debian.org/debian unstable/main arm64 libnghttp3-9 arm64 1.4.0-1+b1 [59.6 kB] Get: 107 http://deb.debian.org/debian unstable/main arm64 libngtcp2-16 arm64 1.6.0-1 [112 kB] Get: 108 http://deb.debian.org/debian unstable/main arm64 libngtcp2-crypto-gnutls8 arm64 1.6.0-1 [18.5 kB] Get: 109 http://deb.debian.org/debian unstable/main arm64 libpsl5t64 arm64 0.21.2-1.1+b1 [57.1 kB] Get: 110 http://deb.debian.org/debian unstable/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b5 [56.8 kB] Get: 111 http://deb.debian.org/debian unstable/main arm64 libssh2-1t64 arm64 1.11.1-1 [235 kB] Get: 112 http://deb.debian.org/debian unstable/main arm64 libcurl3t64-gnutls arm64 8.11.0-1 [331 kB] Get: 113 http://deb.debian.org/debian unstable/main arm64 libjson-c5 arm64 0.18+ds-1 [45.2 kB] Get: 114 http://deb.debian.org/debian unstable/main arm64 libdebuginfod1t64 arm64 0.192-4 [31.3 kB] Get: 115 http://deb.debian.org/debian unstable/main arm64 libpython3.12t64 arm64 3.12.7-3 [1982 kB] Get: 116 http://deb.debian.org/debian unstable/main arm64 libsource-highlight-common all 3.1.9-4.3 [77.5 kB] Get: 117 http://deb.debian.org/debian unstable/main arm64 libsource-highlight4t64 arm64 3.1.9-4.3+b1 [294 kB] Get: 118 http://deb.debian.org/debian unstable/main arm64 gdb arm64 15.2-1 [4157 kB] Get: 119 http://deb.debian.org/debian unstable/main arm64 libaec0 arm64 1.1.3-1+b1 [22.5 kB] Get: 120 http://deb.debian.org/debian unstable/main arm64 libblas3 arm64 3.12.0-3+b1 [98.9 kB] Get: 121 http://deb.debian.org/debian unstable/main arm64 libsnappy1v5 arm64 1.2.1-1+b1 [28.7 kB] Get: 122 http://deb.debian.org/debian unstable/main arm64 libblosc1 arm64 1.21.5+ds-1+b2 [39.2 kB] Get: 123 http://deb.debian.org/debian unstable/main arm64 libblosc2-4 arm64 2.15.1+ds-1 [165 kB] Get: 124 http://deb.debian.org/debian unstable/main arm64 libcurl4t64 arm64 8.11.0-1 [322 kB] Get: 125 http://deb.debian.org/debian unstable/main arm64 libdeflate0 arm64 1.22-1 [42.2 kB] Get: 126 http://deb.debian.org/debian unstable/main arm64 libexpat1-dev arm64 2.6.4-1 [143 kB] Get: 127 http://deb.debian.org/debian unstable/main arm64 libfribidi0 arm64 1.0.15-1 [71.8 kB] Get: 128 http://deb.debian.org/debian unstable/main arm64 libgfortran5 arm64 14.2.0-8 [361 kB] Get: 129 http://deb.debian.org/debian unstable/main arm64 libgraphite2-3 arm64 1.3.14-2+b1 [70.4 kB] Get: 130 http://deb.debian.org/debian unstable/main arm64 libharfbuzz0b arm64 10.0.1-1 [441 kB] Get: 131 http://deb.debian.org/debian unstable/main arm64 libsz2 arm64 1.1.3-1+b1 [8044 B] Get: 132 http://deb.debian.org/debian unstable/main arm64 libhdf5-103-1t64 arm64 1.10.10+repack-4 [1050 kB] Get: 133 http://deb.debian.org/debian unstable/main arm64 libhdf5-hl-100t64 arm64 1.10.10+repack-4 [60.9 kB] Get: 134 http://deb.debian.org/debian unstable/main arm64 libimagequant0 arm64 2.18.0-1+b2 [34.6 kB] Get: 135 http://deb.debian.org/debian unstable/main arm64 libjbig0 arm64 2.1-6.1+b2 [30.4 kB] Get: 136 http://deb.debian.org/debian unstable/main arm64 libjpeg62-turbo arm64 1:2.1.5-3+b1 [173 kB] Get: 137 http://deb.debian.org/debian unstable/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 138 http://deb.debian.org/debian unstable/main arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 139 http://deb.debian.org/debian unstable/main arm64 libjs-mathjax all 2.7.9+dfsg-1 [5667 kB] Get: 140 http://deb.debian.org/debian unstable/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 141 http://deb.debian.org/debian unstable/main arm64 libjs-sphinxdoc all 7.4.7-4 [158 kB] Get: 142 http://deb.debian.org/debian unstable/main arm64 libjson-perl all 4.10000-1 [87.5 kB] Get: 143 http://deb.debian.org/debian unstable/main arm64 liblapack3 arm64 3.12.0-3+b1 [1812 kB] Get: 144 http://deb.debian.org/debian unstable/main arm64 liblbfgsb0 arm64 3.0+dfsg.4-1+b2 [25.6 kB] Get: 145 http://deb.debian.org/debian unstable/main arm64 liblcms2-2 arm64 2.16-2 [151 kB] Get: 146 http://deb.debian.org/debian unstable/main arm64 liblerc4 arm64 4.0.0+ds-5 [146 kB] Get: 147 http://deb.debian.org/debian unstable/main arm64 liblua5.4-0 arm64 5.4.6-3+b2 [133 kB] Get: 148 http://deb.debian.org/debian unstable/main arm64 liblzo2-2 arm64 2.10-3+b1 [49.6 kB] Get: 149 http://deb.debian.org/debian unstable/main arm64 libnetcdf19t64 arm64 1:4.9.2-7 [444 kB] Get: 150 http://deb.debian.org/debian unstable/main arm64 libnorm1t64 arm64 1.5.9+dfsg-3.1+b1 [205 kB] Get: 151 http://deb.debian.org/debian unstable/main arm64 libnuma1 arm64 2.0.18-1+b1 [21.8 kB] Get: 152 http://deb.debian.org/debian unstable/main arm64 libopenjp2-7 arm64 2.5.0-2+b4 [185 kB] Get: 153 http://deb.debian.org/debian unstable/main arm64 libpgm-5.3-0t64 arm64 5.3.128~dfsg-2.1+b1 [152 kB] Get: 154 http://deb.debian.org/debian unstable/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] Get: 155 http://deb.debian.org/debian unstable/main arm64 libpython3.12-dev arm64 3.12.7-3 [4792 kB] Get: 156 http://deb.debian.org/debian unstable/main arm64 libpython3-dev arm64 3.12.6-1 [9952 B] Get: 157 http://deb.debian.org/debian unstable/main arm64 libpython3-all-dev arm64 3.12.6-1 [1064 B] Get: 158 http://deb.debian.org/debian unstable/main arm64 libqhull-r8.0 arm64 2020.2-6+b2 [229 kB] Get: 159 http://deb.debian.org/debian unstable/main arm64 libraqm0 arm64 0.10.1-1+b2 [13.8 kB] Get: 160 http://deb.debian.org/debian unstable/main arm64 libsharpyuv0 arm64 1.4.0-0.1+b1 [112 kB] Get: 161 http://deb.debian.org/debian unstable/main arm64 libsodium23 arm64 1.0.18-1+b2 [121 kB] Get: 162 http://deb.debian.org/debian unstable/main arm64 libwebp7 arm64 1.4.0-0.1+b1 [268 kB] Get: 163 http://deb.debian.org/debian unstable/main arm64 libtiff6 arm64 4.5.1+git230720-5 [309 kB] Get: 164 http://deb.debian.org/debian unstable/main arm64 libwebpdemux2 arm64 1.4.0-0.1+b1 [110 kB] Get: 165 http://deb.debian.org/debian unstable/main arm64 libwebpmux3 arm64 1.4.0-0.1+b1 [122 kB] Get: 166 http://deb.debian.org/debian unstable/main arm64 libxslt1.1 arm64 1.1.35-1.1+b1 [222 kB] Get: 167 http://deb.debian.org/debian unstable/main arm64 libyaml-0-2 arm64 0.2.5-1+b2 [49.3 kB] Get: 168 http://deb.debian.org/debian unstable/main arm64 libzmq5 arm64 4.3.5-1+b3 [253 kB] Get: 169 http://deb.debian.org/debian unstable/main arm64 pandoc-data all 3.1.11.1-3 [459 kB] Get: 170 http://deb.debian.org/debian unstable/main arm64 pandoc arm64 3.1.11.1+ds-2 [26.2 MB] Get: 171 http://deb.debian.org/debian unstable/main arm64 python-babel-localedata all 2.14.0-1 [5701 kB] Get: 172 http://deb.debian.org/debian unstable/main arm64 python-matplotlib-data all 3.8.3-3 [2731 kB] Get: 173 http://deb.debian.org/debian unstable/main arm64 python-tables-data all 3.10.1-1 [49.5 kB] Get: 174 http://deb.debian.org/debian unstable/main arm64 python-tinycss2-common all 1.3.0-1 [31.9 kB] Get: 175 http://deb.debian.org/debian unstable/main arm64 python3-alabaster all 0.7.16-0.1 [27.9 kB] Get: 176 http://deb.debian.org/debian unstable/main arm64 python3-all arm64 3.12.6-1 [1040 B] Get: 177 http://deb.debian.org/debian unstable/main arm64 python3.12-dev arm64 3.12.7-3 [505 kB] Get: 178 http://deb.debian.org/debian unstable/main arm64 python3-dev arm64 3.12.6-1 [26.1 kB] Get: 179 http://deb.debian.org/debian unstable/main arm64 python3-all-dev arm64 3.12.6-1 [1068 B] Get: 180 http://deb.debian.org/debian unstable/main arm64 python3-appdirs all 1.4.4-4 [12.5 kB] Get: 181 http://deb.debian.org/debian unstable/main arm64 python3-asttokens all 2.4.1-2 [20.5 kB] Get: 182 http://deb.debian.org/debian unstable/main arm64 python3-attr all 24.2.0-1 [68.4 kB] Get: 183 http://deb.debian.org/debian unstable/main arm64 python3-tz all 2024.1-2 [30.9 kB] Get: 184 http://deb.debian.org/debian unstable/main arm64 python3-babel all 2.14.0-1 [111 kB] Get: 185 http://deb.debian.org/debian unstable/main arm64 python3-webencodings all 0.5.1-5 [11.1 kB] Get: 186 http://deb.debian.org/debian unstable/main arm64 python3-html5lib all 1.2-1 [92.2 kB] Get: 187 http://deb.debian.org/debian unstable/main arm64 python3-bleach all 6.2.0-1 [51.2 kB] Get: 188 http://deb.debian.org/debian unstable/main arm64 python3-brotli arm64 1.1.0-2+b5 [307 kB] Get: 189 http://deb.debian.org/debian unstable/main arm64 python3-soupsieve all 2.6-1 [38.3 kB] Get: 190 http://deb.debian.org/debian unstable/main arm64 python3-bs4 all 4.12.3-3 [133 kB] Get: 191 http://deb.debian.org/debian unstable/main arm64 python3-certifi all 2024.8.30+dfsg-1 [9576 B] Get: 192 http://deb.debian.org/debian unstable/main arm64 python3-cffi-backend arm64 1.17.1-2 [87.2 kB] Get: 193 http://deb.debian.org/debian unstable/main arm64 python3-numpy arm64 1:1.26.4+ds-11 [3351 kB] Get: 194 http://deb.debian.org/debian unstable/main arm64 python3-cftime arm64 1.6.4-1+b2 [178 kB] Get: 195 http://deb.debian.org/debian unstable/main arm64 python3-chardet all 5.2.0+dfsg-1 [107 kB] Get: 196 http://deb.debian.org/debian unstable/main arm64 python3-charset-normalizer arm64 3.4.0-1 [112 kB] Get: 197 http://deb.debian.org/debian unstable/main arm64 python3-traitlets all 5.14.3+really5.14.3-1 [70.9 kB] Get: 198 http://deb.debian.org/debian unstable/main arm64 python3-comm all 0.2.1-1 [8104 B] Get: 199 http://deb.debian.org/debian unstable/main arm64 python3-contourpy arm64 1.3.0-2 [191 kB] Get: 200 http://deb.debian.org/debian unstable/main arm64 python3-coverage arm64 7.6.0+dfsg1-2 [175 kB] Get: 201 http://deb.debian.org/debian unstable/main arm64 python3-cpuinfo all 9.0.0+git20221119-2 [23.4 kB] Get: 202 http://deb.debian.org/debian unstable/main arm64 python3-cycler all 0.12.1-1 [9496 B] Get: 203 http://deb.debian.org/debian unstable/main arm64 python3-dateutil all 2.9.0-3 [79.3 kB] Get: 204 http://deb.debian.org/debian unstable/main arm64 python3-debugpy arm64 1.8.8+ds-1 [836 kB] Get: 205 http://deb.debian.org/debian unstable/main arm64 python3-decorator all 5.1.1-5 [15.1 kB] Get: 206 http://deb.debian.org/debian unstable/main arm64 python3-defusedxml all 0.7.1-2 [43.3 kB] Get: 207 http://deb.debian.org/debian unstable/main arm64 python3-roman all 4.2-1 [10.4 kB] Get: 208 http://deb.debian.org/debian unstable/main arm64 python3-docutils all 0.21.2+dfsg-2 [403 kB] Get: 209 http://deb.debian.org/debian unstable/main arm64 python3-executing all 2.1.0-0.1 [23.9 kB] Get: 210 http://deb.debian.org/debian unstable/main arm64 python3-fastjsonschema all 2.20.0-1 [21.8 kB] Get: 211 http://deb.debian.org/debian unstable/main arm64 python3-six all 1.16.0-7 [16.4 kB] Get: 212 http://deb.debian.org/debian unstable/main arm64 python3-fs all 2.4.16-4 [95.4 kB] Get: 213 http://deb.debian.org/debian unstable/main arm64 python3-lxml arm64 5.3.0-1 [1096 kB] Get: 214 http://deb.debian.org/debian unstable/main arm64 python3-lz4 arm64 4.0.2+dfsg-1+b5 [25.3 kB] Get: 215 http://deb.debian.org/debian unstable/main arm64 python3-scipy arm64 1.13.1-5 [15.4 MB] Get: 216 http://deb.debian.org/debian unstable/main arm64 python3-mpmath all 1.3.0-1 [419 kB] Get: 217 http://deb.debian.org/debian unstable/main arm64 python3-sympy all 1.13.3-1 [4147 kB] Get: 218 http://deb.debian.org/debian unstable/main arm64 python3-ufolib2 all 0.16.1+dfsg1-1 [32.9 kB] Get: 219 http://deb.debian.org/debian unstable/main arm64 unicode-data all 15.1.0-1 [8547 kB] Get: 220 http://deb.debian.org/debian unstable/main arm64 python3-fonttools arm64 4.54.1-4 [1356 kB] Get: 221 http://deb.debian.org/debian unstable/main arm64 python3-gsd arm64 3.3.0-1+b2 [192 kB] Get: 222 http://deb.debian.org/debian unstable/main arm64 python3-idna all 3.8-2 [41.6 kB] Get: 223 http://deb.debian.org/debian unstable/main arm64 python3-imagesize all 1.4.1-1 [6688 B] Get: 224 http://deb.debian.org/debian unstable/main arm64 python3-parso all 0.8.3-1 [67.4 kB] Get: 225 http://deb.debian.org/debian unstable/main arm64 python3-typeshed all 0.0~git20231111.6764465-3 [1258 kB] Get: 226 http://deb.debian.org/debian unstable/main arm64 python3-jedi all 0.19.1+ds1-1 [691 kB] Get: 227 http://deb.debian.org/debian unstable/main arm64 python3-matplotlib-inline all 0.1.6-2 [8652 B] Get: 228 http://deb.debian.org/debian unstable/main arm64 python3-wcwidth all 0.2.13+dfsg1-1 [24.9 kB] Get: 229 http://deb.debian.org/debian unstable/main arm64 python3-prompt-toolkit all 3.0.48-1 [277 kB] Get: 230 http://deb.debian.org/debian unstable/main arm64 python3-pygments all 2.18.0+dfsg-1 [836 kB] Get: 231 http://deb.debian.org/debian unstable/main arm64 python3-pure-eval all 0.2.3-1 [11.2 kB] Get: 232 http://deb.debian.org/debian unstable/main arm64 python3-stack-data all 0.6.3-1 [21.6 kB] Get: 233 http://deb.debian.org/debian unstable/main arm64 python3-ptyprocess all 0.7.0-6 [14.5 kB] Get: 234 http://deb.debian.org/debian unstable/main arm64 python3-pexpect all 4.9-3 [55.6 kB] Get: 235 http://deb.debian.org/debian unstable/main arm64 python3-ipython all 8.29.0-1 [567 kB] Get: 236 http://deb.debian.org/debian unstable/main arm64 python3-platformdirs all 4.3.6-1 [16.6 kB] Get: 237 http://deb.debian.org/debian unstable/main arm64 python3-jupyter-core all 5.7.2-4 [35.1 kB] Get: 238 http://deb.debian.org/debian unstable/main arm64 python3-psutil arm64 5.9.8-2+b1 [226 kB] Get: 239 http://deb.debian.org/debian unstable/main arm64 python3-tornado arm64 6.4.1-3 [349 kB] Get: 240 http://deb.debian.org/debian unstable/main arm64 python3-py all 1.11.0-2 [88.7 kB] Get: 241 http://deb.debian.org/debian unstable/main arm64 python3-zmq arm64 24.0.1-5+b3 [256 kB] Get: 242 http://deb.debian.org/debian unstable/main arm64 python3-jupyter-client all 8.6.2-3 [91.5 kB] Get: 243 http://deb.debian.org/debian unstable/main arm64 python3-nest-asyncio all 1.5.4-1 [6248 B] Get: 244 http://deb.debian.org/debian unstable/main arm64 python3-packaging all 24.1-1 [45.8 kB] Get: 245 http://deb.debian.org/debian unstable/main arm64 python3-ipykernel all 6.29.5-1 [102 kB] Get: 246 http://deb.debian.org/debian unstable/main arm64 python3-markupsafe arm64 2.1.5-1+b2 [13.8 kB] Get: 247 http://deb.debian.org/debian unstable/main arm64 python3-jinja2 all 3.1.3-1 [119 kB] Get: 248 http://deb.debian.org/debian unstable/main arm64 python3-joblib all 1.3.2-5 [216 kB] Get: 249 http://deb.debian.org/debian unstable/main arm64 python3-rpds-py arm64 0.21.0-1 [223 kB] Get: 250 http://deb.debian.org/debian unstable/main arm64 python3-referencing all 0.35.1-1 [23.5 kB] Get: 251 http://deb.debian.org/debian unstable/main arm64 python3-jsonschema-specifications all 2023.12.1-2 [9020 B] Get: 252 http://deb.debian.org/debian unstable/main arm64 python3-jsonschema all 4.19.2-5 [71.4 kB] Get: 253 http://deb.debian.org/debian unstable/main arm64 python3-jupyterlab-pygments all 0.2.2-3 [6096 B] Get: 254 http://deb.debian.org/debian unstable/main arm64 python3-kiwisolver arm64 1.4.7-2 [56.7 kB] Get: 255 http://deb.debian.org/debian unstable/main arm64 python3-pil arm64 10.4.0-1 [480 kB] Get: 256 http://deb.debian.org/debian unstable/main arm64 python3.12-tk arm64 3.12.7-3 [111 kB] Get: 257 http://deb.debian.org/debian unstable/main arm64 python3.13-tk arm64 3.13.0-1 [101 kB] Get: 258 http://deb.debian.org/debian unstable/main arm64 python3-tk arm64 3.12.6-1 [9428 B] Get: 259 http://deb.debian.org/debian unstable/main arm64 python3-pil.imagetk arm64 10.4.0-1 [79.4 kB] Get: 260 http://deb.debian.org/debian unstable/main arm64 python3-pyparsing all 3.1.2-1 [146 kB] Get: 261 http://deb.debian.org/debian unstable/main arm64 python3-matplotlib arm64 3.8.3-3 [5509 kB] Get: 262 http://deb.debian.org/debian unstable/main arm64 python3-mistune all 3.0.2-2 [33.2 kB] Get: 263 http://deb.debian.org/debian unstable/main arm64 sphinx-rtd-theme-common all 3.0.1+dfsg-1 [1022 kB] Get: 264 http://deb.debian.org/debian unstable/main arm64 sphinx-common all 7.4.7-4 [731 kB] Get: 265 http://deb.debian.org/debian unstable/main arm64 python3-urllib3 all 2.0.7-2 [111 kB] Get: 266 http://deb.debian.org/debian unstable/main arm64 python3-requests all 2.32.3+dfsg-1 [71.9 kB] Get: 267 http://deb.debian.org/debian unstable/main arm64 python3-snowballstemmer all 2.2.0-4 [58.0 kB] Get: 268 http://deb.debian.org/debian unstable/main arm64 python3-sphinx all 7.4.7-4 [588 kB] Get: 269 http://deb.debian.org/debian unstable/main arm64 python3-sphinxcontrib.jquery all 4.1-5 [7348 B] Get: 270 http://deb.debian.org/debian unstable/main arm64 python3-sphinx-rtd-theme all 3.0.1+dfsg-1 [29.5 kB] Get: 271 http://deb.debian.org/debian unstable/main arm64 python3-msmb-theme all 1.2.0-4 [33.8 kB] Get: 272 http://deb.debian.org/debian unstable/main arm64 python3-nbformat all 5.9.1-1 [45.1 kB] Get: 273 http://deb.debian.org/debian unstable/main arm64 python3-nbclient all 0.8.0-1 [64.0 kB] Get: 274 http://deb.debian.org/debian unstable/main arm64 python3-pandocfilters all 1.5.1-1 [23.7 kB] Get: 275 http://deb.debian.org/debian unstable/main arm64 python3-tinycss2 all 1.3.0-1 [22.1 kB] Get: 276 http://deb.debian.org/debian unstable/main arm64 python3-nbconvert all 7.16.4-2 [158 kB] Get: 277 http://deb.debian.org/debian unstable/main arm64 python3-nbsphinx all 0.9.4+ds-1.1 [39.6 kB] Get: 278 http://deb.debian.org/debian unstable/main arm64 python3-nbsphinx-link all 1.3.0-4 [6264 B] Get: 279 http://deb.debian.org/debian unstable/main arm64 python3-netcdf4 arm64 1.7.2-1+b1 [525 kB] Get: 280 http://deb.debian.org/debian unstable/main arm64 python3-networkx all 3.2.1-4 [14.2 MB] Get: 281 http://deb.debian.org/debian unstable/main arm64 python3-numexpr arm64 2.10.1-2+b2 [121 kB] Get: 282 http://deb.debian.org/debian unstable/main arm64 python3-tabulate all 0.9.0-1 [45.9 kB] Get: 283 http://deb.debian.org/debian unstable/main arm64 python3-numpydoc all 1.6.0-2 [49.6 kB] Get: 284 http://deb.debian.org/debian unstable/main arm64 python3-pandas-lib arm64 2.2.3+dfsg-5 [3746 kB] Get: 285 http://deb.debian.org/debian unstable/main arm64 python3-pandas all 2.2.3+dfsg-5 [3096 kB] Get: 286 http://deb.debian.org/debian unstable/main arm64 python3-threadpoolctl all 3.1.0-1 [21.2 kB] Get: 287 http://deb.debian.org/debian unstable/main arm64 python3-sklearn-lib arm64 1.4.2+dfsg-6 [3213 kB] Get: 288 http://deb.debian.org/debian unstable/main arm64 python3-sklearn all 1.4.2+dfsg-6 [2248 kB] Get: 289 http://deb.debian.org/debian unstable/main arm64 python3-tables-lib arm64 3.10.1-1 [435 kB] Get: 290 http://deb.debian.org/debian unstable/main arm64 python3-tables all 3.10.1-1 [355 kB] Get: 291 http://deb.debian.org/debian unstable/main arm64 python3-versioneer all 0.29-1 [43.0 kB] Fetched 192 MB in 1s (144 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 ... 20088 files and directories currently installed.) Preparing to unpack .../0-fonts-lato_2.015-1_all.deb ... Unpacking fonts-lato (2.015-1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../1-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... 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_0.192-4_all.deb ... Unpacking libdebuginfod-common (0.192-4) ... Selecting previously unselected package libpython3.12-minimal:arm64. Preparing to unpack .../4-libpython3.12-minimal_3.12.7-3_arm64.deb ... Unpacking libpython3.12-minimal:arm64 (3.12.7-3) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../5-libexpat1_2.6.4-1_arm64.deb ... Unpacking libexpat1:arm64 (2.6.4-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../6-python3.12-minimal_3.12.7-3_arm64.deb ... Unpacking python3.12-minimal (3.12.7-3) ... Setting up libpython3.12-minimal:arm64 (3.12.7-3) ... Setting up libexpat1:arm64 (2.6.4-1) ... Setting up python3.12-minimal (3.12.7-3) ... 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 ... 20520 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.6-1_arm64.deb ... Unpacking python3-minimal (3.12.6-1) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../03-tzdata_2024b-3_all.deb ... Unpacking tzdata (2024b-3) ... Selecting previously unselected package libkrb5support0:arm64. Preparing to unpack .../04-libkrb5support0_1.21.3-3_arm64.deb ... Unpacking libkrb5support0:arm64 (1.21.3-3) ... Selecting previously unselected package libcom-err2:arm64. Preparing to unpack .../05-libcom-err2_1.47.1-1+b1_arm64.deb ... Unpacking libcom-err2:arm64 (1.47.1-1+b1) ... Selecting previously unselected package libk5crypto3:arm64. Preparing to unpack .../06-libk5crypto3_1.21.3-3_arm64.deb ... Unpacking libk5crypto3:arm64 (1.21.3-3) ... Selecting previously unselected package libkeyutils1:arm64. Preparing to unpack .../07-libkeyutils1_1.6.3-4_arm64.deb ... Unpacking libkeyutils1:arm64 (1.6.3-4) ... Selecting previously unselected package libkrb5-3:arm64. Preparing to unpack .../08-libkrb5-3_1.21.3-3_arm64.deb ... Unpacking libkrb5-3:arm64 (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:arm64. Preparing to unpack .../09-libgssapi-krb5-2_1.21.3-3_arm64.deb ... Unpacking libgssapi-krb5-2:arm64 (1.21.3-3) ... Selecting previously unselected package libtirpc-common. Preparing to unpack .../10-libtirpc-common_1.3.4+ds-1.3_all.deb ... Unpacking libtirpc-common (1.3.4+ds-1.3) ... Selecting previously unselected package libtirpc3t64:arm64. Preparing to unpack .../11-libtirpc3t64_1.3.4+ds-1.3+b1_arm64.deb ... Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3 to /lib/aarch64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3.0.0 to /lib/aarch64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:arm64 (1.3.4+ds-1.3+b1) ... Selecting previously unselected package libnsl2:arm64. Preparing to unpack .../12-libnsl2_1.3.0-3+b3_arm64.deb ... Unpacking libnsl2:arm64 (1.3.0-3+b3) ... Selecting previously unselected package readline-common. Preparing to unpack .../13-readline-common_8.2-5_all.deb ... Unpacking readline-common (8.2-5) ... Selecting previously unselected package libreadline8t64:arm64. Preparing to unpack .../14-libreadline8t64_8.2-5_arm64.deb ... Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:arm64 (8.2-5) ... Selecting previously unselected package libpython3.12-stdlib:arm64. Preparing to unpack .../15-libpython3.12-stdlib_3.12.7-3_arm64.deb ... Unpacking libpython3.12-stdlib:arm64 (3.12.7-3) ... Selecting previously unselected package python3.12. Preparing to unpack .../16-python3.12_3.12.7-3_arm64.deb ... Unpacking python3.12 (3.12.7-3) ... Selecting previously unselected package libpython3-stdlib:arm64. Preparing to unpack .../17-libpython3-stdlib_3.12.6-1_arm64.deb ... Unpacking libpython3-stdlib:arm64 (3.12.6-1) ... Setting up python3-minimal (3.12.6-1) ... 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 ... 21582 files and directories currently installed.) Preparing to unpack .../000-python3_3.12.6-1_arm64.deb ... Unpacking python3 (3.12.6-1) ... 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%3a4.0.4-6_arm64.deb ... Unpacking libproc2-0:arm64 (2:4.0.4-6) ... Selecting previously unselected package procps. Preparing to unpack .../003-procps_2%3a4.0.4-6_arm64.deb ... Unpacking procps (2:4.0.4-6) ... Selecting previously unselected package openssl. Preparing to unpack .../004-openssl_3.3.2-2_arm64.deb ... Unpacking openssl (3.3.2-2) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../005-ca-certificates_20240203_all.deb ... Unpacking ca-certificates (20240203) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../006-libmagic-mgc_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../007-libmagic1t64_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../008-file_1%3a5.45-3+b1_arm64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../009-gettext-base_0.22.5-2_arm64.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../010-libuchardet0_0.0.8-1+b2_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../011-groff-base_1.23.0-5_arm64.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../012-bsdextrautils_2.40.2-10_arm64.deb ... Unpacking bsdextrautils (2.40.2-10) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../013-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../014-man-db_2.13.0-1_arm64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../015-m4_1.4.19-4_arm64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../016-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... 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_0.22.5-2_all.deb ... Unpacking autopoint (0.22.5-2) ... Selecting previously unselected package libtcl8.6:arm64. Preparing to unpack .../020-libtcl8.6_8.6.15+dfsg-2_arm64.deb ... Unpacking libtcl8.6:arm64 (8.6.15+dfsg-2) ... Selecting previously unselected package libbrotli1:arm64. Preparing to unpack .../021-libbrotli1_1.1.0-2+b5_arm64.deb ... Unpacking libbrotli1:arm64 (1.1.0-2+b5) ... Selecting previously unselected package libpng16-16t64:arm64. Preparing to unpack .../022-libpng16-16t64_1.6.44-2_arm64.deb ... Unpacking libpng16-16t64:arm64 (1.6.44-2) ... Selecting previously unselected package libfreetype6:arm64. Preparing to unpack .../023-libfreetype6_2.13.3+dfsg-1_arm64.deb ... Unpacking libfreetype6:arm64 (2.13.3+dfsg-1) ... Selecting previously unselected package fonts-dejavu-mono. Preparing to unpack .../024-fonts-dejavu-mono_2.37-8_all.deb ... Unpacking fonts-dejavu-mono (2.37-8) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../025-fonts-dejavu-core_2.37-8_all.deb ... Unpacking fonts-dejavu-core (2.37-8) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../026-fontconfig-config_2.15.0-1.1+b1_arm64.deb ... Unpacking fontconfig-config (2.15.0-1.1+b1) ... Selecting previously unselected package libfontconfig1:arm64. Preparing to unpack .../027-libfontconfig1_2.15.0-1.1+b1_arm64.deb ... Unpacking libfontconfig1:arm64 (2.15.0-1.1+b1) ... Selecting previously unselected package libxau6:arm64. Preparing to unpack .../028-libxau6_1%3a1.0.11-1_arm64.deb ... Unpacking libxau6:arm64 (1:1.0.11-1) ... Selecting previously unselected package libxdmcp6:arm64. Preparing to unpack .../029-libxdmcp6_1%3a1.1.2-3+b2_arm64.deb ... Unpacking libxdmcp6:arm64 (1:1.1.2-3+b2) ... Selecting previously unselected package libxcb1:arm64. Preparing to unpack .../030-libxcb1_1.17.0-2+b1_arm64.deb ... Unpacking libxcb1:arm64 (1.17.0-2+b1) ... Selecting previously unselected package libx11-data. Preparing to unpack .../031-libx11-data_2%3a1.8.10-2_all.deb ... Unpacking libx11-data (2:1.8.10-2) ... Selecting previously unselected package libx11-6:arm64. Preparing to unpack .../032-libx11-6_2%3a1.8.10-2_arm64.deb ... Unpacking libx11-6:arm64 (2:1.8.10-2) ... Selecting previously unselected package libxrender1:arm64. Preparing to unpack .../033-libxrender1_1%3a0.9.10-1.1+b2_arm64.deb ... 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Setting up liblcms2-2:arm64 (2.16-2) ... Setting up libnorm1t64:arm64 (1.5.9+dfsg-3.1+b1) ... Setting up libsharpyuv0:arm64 (1.4.0-0.1+b1) ... Setting up libxau6:arm64 (1:1.0.11-1) ... Setting up libxdmcp6:arm64 (1:1.1.2-3+b2) ... Setting up libkeyutils1:arm64 (1.6.3-4) ... Setting up libxcb1:arm64 (1.17.0-2+b1) ... Setting up fonts-lato (2.015-1) ... Setting up fonts-mathjax (2.7.9+dfsg-1) ... Setting up libsodium23:arm64 (1.0.18-1+b2) ... Setting up libicu72:arm64 (72.1-5+b1) ... Setting up liblerc4:arm64 (4.0.0+ds-5) ... Setting up bsdextrautils (2.40.2-10) ... Setting up libjs-mathjax (2.7.9+dfsg-1) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libyaml-0-2:arm64 (0.2.5-1+b2) ... Setting up libtirpc-common (1.3.4+ds-1.3) ... Setting up fonts-lyx (2.4.2.1-1) ... Setting up libdebhelper-perl (13.20) ... Setting up libbrotli1:arm64 (1.1.0-2+b5) ... Setting up libmagic1t64:arm64 (1:5.45-3+b1) ... Setting up x11-common (1:7.7+23.1) ... invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libpsl5t64:arm64 (0.21.2-1.1+b1) ... Setting up libnghttp2-14:arm64 (1.64.0-1) ... Setting up libdeflate0:arm64 (1.22-1) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up libqhull-r8.0:arm64 (2020.2-6+b2) ... Setting up liblzo2-2:arm64 (2.10-3+b1) ... Setting up libcom-err2:arm64 (1.47.1-1+b1) ... Setting up file (1:5.45-3+b1) ... Setting up libjbig0:arm64 (2.1-6.1+b2) ... Setting up libaec0:arm64 (1.1.3-1+b1) ... Setting up libsource-highlight-common (3.1.9-4.3) ... Setting up libelf1t64:arm64 (0.192-4) ... Setting up python-babel-localedata (2.14.0-1) ... Setting up libsnappy1v5:arm64 (1.2.1-1+b1) ... Setting up libkrb5support0:arm64 (1.21.3-3) ... Setting up libdw1t64:arm64 (0.192-4) ... Setting up libsasl2-modules-db:arm64 (2.1.28+dfsg1-8) ... Setting up tzdata (2024b-3) ... Current default time zone: 'Etc/UTC' Local time is now: Mon Dec 15 13:38:00 UTC 2025. Universal Time is now: Mon Dec 15 13:38:00 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up unicode-data (15.1.0-1) ... Setting up libpgm-5.3-0t64:arm64 (5.3.128~dfsg-2.1+b1) ... Setting up libblosc2-4:arm64 (2.15.1+ds-1) ... Setting up autotools-dev (20220109.1) ... Setting up libglib2.0-0t64:arm64 (2.82.2-2) ... No schema files found: doing nothing. Setting up libblas3:arm64 (3.12.0-3+b1) ... 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 (2.6.4-1) ... Setting up libjpeg62-turbo:arm64 (1:2.1.5-3+b1) ... Setting up libx11-data (2:1.8.10-2) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libfribidi0:arm64 (1.0.15-1) ... Setting up libimagequant0:arm64 (2.18.0-1+b2) ... Setting up libproc2-0:arm64 (2:4.0.4-6) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:arm64 (1.6.44-2) ... Setting up libtcl8.6:arm64 (8.6.15+dfsg-2) ... Setting up autopoint (0.22.5-2) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libk5crypto3:arm64 (1.21.3-3) ... Setting up libbabeltrace1:arm64 (1.5.11-4) ... Setting up libsasl2-2:arm64 (2.1.28+dfsg1-8) ... Setting up libgfortran5:arm64 (14.2.0-8) ... Setting up autoconf (2.72-3) ... Setting up libnghttp3-9:arm64 (1.4.0-1+b1) ... Setting up libwebp7:arm64 (1.4.0-0.1+b1) ... Setting up zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libnuma1:arm64 (2.0.18-1+b1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libtiff6:arm64 (4.5.1+git230720-5) ... Setting up libuchardet0:arm64 (0.0.8-1+b2) ... Setting up procps (2:4.0.4-6) ... Setting up python-tinycss2-common (1.3.0-1) ... Setting up libjson-perl (4.10000-1) ... Setting up libblosc1:arm64 (1.21.5+ds-1+b2) ... Setting up liblua5.4-0:arm64 (5.4.6-3+b2) ... Setting up libopenjp2-7:arm64 (2.5.0-2+b4) ... Setting up libx11-6:arm64 (2:1.8.10-2) ... Setting up netbase (6.4) ... Setting up libngtcp2-16:arm64 (1.6.0-1) ... Setting up sgml-base (1.31) ... Setting up libkrb5-3:arm64 (1.21.3-3) ... Setting up libssh2-1t64:arm64 (1.11.1-1) ... Setting up pandoc-data (3.1.11.1-3) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up python-matplotlib-data (3.8.3-3) ... Setting up openssl (3.3.2-2) ... Setting up libwebpmux3:arm64 (1.4.0-0.1+b1) ... Setting up libjson-c5:arm64 (0.18+ds-1) ... Setting up readline-common (8.2-5) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2) ... Setting up python-tables-data (3.10.1-1) ... Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... Setting up sphinx-rtd-theme-common (3.0.1+dfsg-1) ... Setting up libngtcp2-crypto-gnutls8:arm64 (1.6.0-1) ... Setting up libsz2:arm64 (1.1.3-1+b1) ... 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 (1.14.0-1) ... Setting up liblapack3:arm64 (3.12.0-3+b1) ... 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 gettext (0.22.5-2) ... Setting up libxrender1:arm64 (1:0.9.10-1.1+b2) ... Setting up libtool (2.4.7-8) ... Setting up fontconfig-config (2.15.0-1.1+b1) ... Setting up libwebpdemux2:arm64 (1.4.0-0.1+b1) ... Setting up libxext6:arm64 (2:1.3.4-1+b2) ... Setting up libsource-highlight4t64:arm64 (3.1.9-4.3+b1) ... Setting up libldap-2.5-0:arm64 (2.5.18+dfsg-3+b1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up pandoc (3.1.11.1+ds-2) ... Setting up libfreetype6:arm64 (2.13.3+dfsg-1) ... Setting up libgssapi-krb5-2:arm64 (1.21.3-3) ... Setting up ucf (3.0043+nmu1) ... Setting up libjs-sphinxdoc (7.4.7-4) ... Setting up libreadline8t64:arm64 (8.2-5) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... Setting up xml-core (0.19) ... Setting up libxslt1.1:arm64 (1.1.35-1.1+b1) ... Setting up libharfbuzz0b:arm64 (10.0.1-1) ... Setting up libxss1:arm64 (1:1.2.3-1+b2) ... Setting up libfontconfig1:arm64 (2.15.0-1.1+b1) ... Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1+b2) ... Setting up libxft2:arm64 (2.3.6-1+b2) ... Setting up libzmq5:arm64 (4.3.5-1+b3) ... Setting up libdebuginfod-common (0.192-4) ... Setting up libcurl4t64:arm64 (8.11.0-1) ... Setting up libtirpc3t64:arm64 (1.3.4+ds-1.3+b1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libtk8.6:arm64 (8.6.15-1) ... Setting up python3.12-tk (3.12.7-3) ... Setting up libcurl3t64-gnutls:arm64 (8.11.0-1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up python3.13-tk (3.13.0-1) ... Setting up libraqm0:arm64 (0.10.1-1+b2) ... Setting up sphinx-common (7.4.7-4) ... Setting up libnsl2:arm64 (1.3.0-3+b3) ... Setting up libhdf5-103-1t64:arm64 (1.10.10+repack-4) ... Setting up libhdf5-hl-100t64:arm64 (1.10.10+repack-4) ... Setting up libdebuginfod1t64:arm64 (0.192-4) ... Setting up tk8.6-blt2.5 (2.5.3+dfsg-7+b1) ... Setting up libnetcdf19t64:arm64 (1:4.9.2-7) ... Setting up libpython3.12-stdlib:arm64 (3.12.7-3) ... Setting up blt (2.5.3+dfsg-7+b1) ... Setting up python3.12 (3.12.7-3) ... Setting up debhelper (13.20) ... Setting up libpython3.12t64:arm64 (3.12.7-3) ... Setting up gdb (15.2-1) ... Setting up libpython3-stdlib:arm64 (3.12.6-1) ... Setting up python3 (3.12.6-1) ... 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Setting up python3-ptyprocess (0.7.0-6) ... Setting up python3-prompt-toolkit (3.0.48-1) ... Setting up python3-more-itertools (10.5.0-1) ... Setting up python3-sympy (1.13.3-1) ... Setting up python3-attr (24.2.0-1) ... Setting up python3-tornado (6.4.1-3) ... Setting up python3-pure-eval (0.2.3-1) ... Setting up python3-tinycss2 (1.3.0-1) ... Setting up libpython3-dev:arm64 (3.12.6-1) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up python3-parso (0.8.3-1) ... Setting up python3-lz4 (4.0.2+dfsg-1+b5) ... Setting up python3-defusedxml (0.7.1-2) ... Setting up python3-asttokens (2.4.1-2) ... Setting up python3-charset-normalizer (3.4.0-1) ... Setting up python3-alabaster (0.7.16-0.1) ... Setting up python3-typeguard (4.4.1-1) ... Setting up python3-threadpoolctl (3.1.0-1) ... Setting up python3-tabulate (0.9.0-1) ... Setting up python3-all (3.12.6-1) ... Setting up python3-coverage (7.6.0+dfsg1-2) ... Setting up python3-tk:arm64 (3.12.6-1) ... Setting up python3-debugpy (1.8.8+ds-1) ... Setting up python3-bs4 (4.12.3-3) ... Setting up python3-bleach (6.2.0-1) ... Setting up python3-matplotlib-inline (0.1.6-2) ... Setting up python3-comm (0.2.1-1) ... Setting up python3-inflect (7.3.1-2) ... Setting up python3-pil.imagetk:arm64 (10.4.0-1) ... Setting up python3-executing (2.1.0-0.1) ... Setting up libpython3-all-dev:arm64 (3.12.6-1) ... Setting up python3-jaraco.text (4.0.0-1) ... Setting up python3-pexpect (4.9-3) ... Setting up python3-dev (3.12.6-1) ... Setting up python3-stack-data (0.6.3-1) ... Setting up python3-referencing (0.35.1-1) ... Setting up python3-pkg-resources (75.2.0-1) ... Setting up python3-all-dev (3.12.6-1) ... Setting up python3-setuptools (75.2.0-1) ... Setting up python3-py (1.11.0-2) ... Setting up python3-jedi (0.19.1+ds1-1) ... Setting up python3-joblib (1.3.2-5) ... Setting up python3-babel (2.14.0-1) ... update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up python3-networkx (3.2.1-4) ... Setting up python3-fs (2.4.16-4) ... Setting up python3-pygments (2.18.0+dfsg-1) ... Setting up python3-chardet (5.2.0+dfsg-1) ... Setting up python3-ipython (8.29.0-1) ... Setting up python3-zmq (24.0.1-5+b3) ... Setting up python3-requests (2.32.3+dfsg-1) ... Setting up python3-numpy (1:1.26.4+ds-11) ... Setting up python3-jupyter-client (8.6.2-3) ... Setting up python3-contourpy (1.3.0-2) ... Setting up python3-jsonschema-specifications (2023.12.1-2) ... Setting up dh-python (6.20241024) ... Setting up python3-scipy (1.13.1-5) ... Setting up python3-tables-lib (3.10.1-1) ... Setting up python3-pandas-lib:arm64 (2.2.3+dfsg-5) ... Setting up python3-sklearn-lib:arm64 (1.4.2+dfsg-6) ... Setting up python3-gsd (3.3.0-1+b2) ... Setting up python3-jupyterlab-pygments (0.2.2-3) ... Setting up python3-pandas (2.2.3+dfsg-5) ... Setting up python3-jsonschema (4.19.2-5) ... Setting up python3-ipykernel (6.29.5-1) ... Setting up python3-sklearn (1.4.2+dfsg-6) ... Setting up python3-cftime (1.6.4-1+b2) ... Setting up python3-numexpr (2.10.1-2+b2) ... Setting up python3-netcdf4 (1.7.2-1+b1) ... Setting up python3-nbformat (5.9.1-1) ... Setting up python3-tables (3.10.1-1) ... Setting up python3-nbclient (0.8.0-1) ... Setting up python3-nbconvert (7.16.4-2) ... Setting up python3-fonttools (4.54.1-4) ... Setting up python3-ufolib2 (0.16.1+dfsg1-1) ... Setting up python3-matplotlib (3.8.3-3) ... Processing triggers for libc-bin (2.40-3) ... Processing triggers for sgml-base (1.31) ... Setting up docutils-common (0.21.2+dfsg-2) ... Processing triggers for sgml-base (1.31) ... Setting up python3-docutils (0.21.2+dfsg-2) ... Setting up python3-sphinx (7.4.7-4) ... Setting up python3-nbsphinx (0.9.4+ds-1.1) ... Setting up python3-sphinxcontrib.jquery (4.1-5) ... Setting up python3-numpydoc (1.6.0-2) ... Setting up python3-nbsphinx-link (1.3.0-4) ... Setting up python3-sphinx-rtd-theme (3.0.1+dfsg-1) ... Setting up python3-msmb-theme (1.2.0-4) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/2563990/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/2563990/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/mdtraj-1.10.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../mdtraj_1.10.1-2_source.changes dpkg-buildpackage: info: source package mdtraj dpkg-buildpackage: info: source version 1.10.1-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Emmanuel Arias dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 dpkg-source: info: using options from mdtraj-1.10.1/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/ debian/rules clean dh clean --with sphinxdoc --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild pybuild --clean -i python{version} -p 3.12 I: pybuild base:311: python3.12 setup.py clean Using built-in specs. COLLECT_GCC=/usr/bin/aarch64-linux-gnu-gcc COLLECT_LTO_WRAPPER=/usr/libexec/gcc/aarch64-linux-gnu/14/lto-wrapper OFFLOAD_TARGET_NAMES=nvptx-none OFFLOAD_TARGET_DEFAULT=1 Target: aarch64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 14.2.0-8' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=aarch64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libquadmath --disable-libquadmath-support --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --enable-fix-cortex-a53-843419 --disable-werror --enable-offload-targets=nvptx-none=/build/reproducible-path/gcc-14-14.2.0/debian/tmp-nvptx/usr --enable-offload-defaulted --without-cuda-driver --enable-checking=release --build=aarch64-linux-gnu --host=aarch64-linux-gnu --target=aarch64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=2 Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 14.2.0 (Debian 14.2.0-8) /build/reproducible-path/mdtraj-1.10.1/basesetup.py:483: UserWarning: Unrecognized setuptools command ('clean'), proceeding with generating Cython sources and expanding templates warnings.warn( warning: mdtraj/formats/dcd/dcdlib.pxd:12:12: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. warning: mdtraj/formats/dcd/dcdlib.pxd:12:16: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. warning: mdtraj/formats/dcd/dcdlib.pxd:12:20: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. performance hint: mdtraj/geometry/src/image_molecules.pxi:15:5: Exception check on 'make_whole' will always require the GIL to be acquired. Possible solutions: 1. Declare 'make_whole' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on 'make_whole' to allow an error code to be returned. performance hint: mdtraj/geometry/src/image_molecules.pxi:36:5: Exception check on 'anchor_dists' will always require the GIL to be acquired. Possible solutions: 1. Declare 'anchor_dists' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on 'anchor_dists' to allow an error code to be returned. performance hint: mdtraj/geometry/src/image_molecules.pxi:68:5: Exception check on 'wrap_mols' will always require the GIL to be acquired. Possible solutions: 1. Declare 'wrap_mols' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on 'wrap_mols' to allow an error code to be returned. C compiler: Attempting to autodetect OpenMP support... Compiler supports OpenMP Attempting to autodetect SSE2 support... Did not detect SSE2 support Attempting to autodetect SSE3 support... Did not detect SSE3 support Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support Attempting to autodetect NEON support... Compiler supports NEON [ 1/10] Cythonizing mdtraj/formats/dcd/dcd.pyx [ 2/10] Cythonizing mdtraj/formats/dtr/dtr.pyx [ 3/10] Cythonizing mdtraj/formats/xtc/trr.pyx [ 4/10] Cythonizing mdtraj/formats/xtc/xtc.pyx [ 5/10] Cythonizing mdtraj/geometry/drid.pyx [ 6/10] Cythonizing mdtraj/geometry/neighborlist.pyx [ 7/10] Cythonizing mdtraj/geometry/neighbors.pyx [ 8/10] Cythonizing mdtraj/geometry/src/_geometry.pyx [ 9/10] Cythonizing mdtraj/rmsd/_lprmsd.pyx [10/10] Cythonizing mdtraj/rmsd/_rmsd.pyx running clean removing '/build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build' (and everything under it) 'build/bdist.linux-aarch64' does not exist -- can't clean it 'build/scripts-3.12' does not exist -- can't clean it rm -rf .pybuild/ find . -name \*.pyc -exec rm {} \; debian/rules execute_after_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/mdtraj-1.10.1' for f in mdtraj/formats/binpos/binpos.c \ mdtraj/formats/dcd/dcd.c \ mdtraj/formats/dtr/dtr.cpp \ mdtraj/formats/tng/tng.c \ mdtraj/formats/xtc/trr.c \ mdtraj/formats/xtc/xtc.c \ mdtraj/geometry/drid.cpp \ mdtraj/geometry/neighborlist.cpp \ mdtraj/geometry/neighbors.cpp \ mdtraj/geometry/src/_geometry.cpp \ mdtraj/rmsd/_lprmsd.cpp \ mdtraj/rmsd/_rmsd.cpp \ mdtraj/version.py; \ do rm -f $f; done rm -rf mdtraj/core/lib rm -rf docs/api/generated rm -rf __pycache__ .pybuild find . -name "lib*.a" -delete make[1]: Leaving directory '/build/reproducible-path/mdtraj-1.10.1' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/python3-mdtraj.substvars debian/python-mdtraj-doc.substvars debian/files rm -fr -- debian/python3-mdtraj/ debian/tmp/ debian/python-mdtraj-doc/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a \( -name autom4te.cache -o -name __pycache__ \) -prune -exec rm -rf {} + \) \) debian/rules binary dh binary --with sphinxdoc --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild pybuild --configure -i python{version} -p 3.12 I: pybuild base:311: python3.12 setup.py config Using built-in specs. COLLECT_GCC=/usr/bin/aarch64-linux-gnu-gcc COLLECT_LTO_WRAPPER=/usr/libexec/gcc/aarch64-linux-gnu/14/lto-wrapper OFFLOAD_TARGET_NAMES=nvptx-none OFFLOAD_TARGET_DEFAULT=1 Target: aarch64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 14.2.0-8' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=aarch64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libquadmath --disable-libquadmath-support --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --enable-fix-cortex-a53-843419 --disable-werror --enable-offload-targets=nvptx-none=/build/reproducible-path/gcc-14-14.2.0/debian/tmp-nvptx/usr --enable-offload-defaulted --without-cuda-driver --enable-checking=release --build=aarch64-linux-gnu --host=aarch64-linux-gnu --target=aarch64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=2 Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 14.2.0 (Debian 14.2.0-8) /build/reproducible-path/mdtraj-1.10.1/basesetup.py:483: UserWarning: Unrecognized setuptools command ('config'), proceeding with generating Cython sources and expanding templates warnings.warn( warning: mdtraj/formats/dcd/dcdlib.pxd:12:12: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. warning: mdtraj/formats/dcd/dcdlib.pxd:12:16: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. warning: mdtraj/formats/dcd/dcdlib.pxd:12:20: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. performance hint: mdtraj/geometry/src/image_molecules.pxi:15:5: Exception check on 'make_whole' will always require the GIL to be acquired. Possible solutions: 1. Declare 'make_whole' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on 'make_whole' to allow an error code to be returned. performance hint: mdtraj/geometry/src/image_molecules.pxi:36:5: Exception check on 'anchor_dists' will always require the GIL to be acquired. Possible solutions: 1. Declare 'anchor_dists' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on 'anchor_dists' to allow an error code to be returned. performance hint: mdtraj/geometry/src/image_molecules.pxi:68:5: Exception check on 'wrap_mols' will always require the GIL to be acquired. Possible solutions: 1. Declare 'wrap_mols' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on 'wrap_mols' to allow an error code to be returned. C compiler: Attempting to autodetect OpenMP support... Compiler supports OpenMP Attempting to autodetect SSE2 support... Did not detect SSE2 support Attempting to autodetect SSE3 support... Did not detect SSE3 support Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support Attempting to autodetect NEON support... Compiler supports NEON [ 1/10] Cythonizing mdtraj/formats/dcd/dcd.pyx [ 2/10] Cythonizing mdtraj/formats/dtr/dtr.pyx [ 3/10] Cythonizing mdtraj/formats/xtc/trr.pyx [ 4/10] Cythonizing mdtraj/formats/xtc/xtc.pyx [ 5/10] Cythonizing mdtraj/geometry/drid.pyx [ 6/10] Cythonizing mdtraj/geometry/neighborlist.pyx [ 7/10] Cythonizing mdtraj/geometry/neighbors.pyx [ 8/10] Cythonizing mdtraj/geometry/src/_geometry.pyx [ 9/10] Cythonizing mdtraj/rmsd/_lprmsd.pyx [10/10] Cythonizing mdtraj/rmsd/_rmsd.pyx running config dh_auto_build -O--buildsystem=pybuild pybuild --build -i python{version} -p 3.12 I: pybuild base:311: /usr/bin/python3 setup.py build Using built-in specs. COLLECT_GCC=/usr/bin/aarch64-linux-gnu-gcc COLLECT_LTO_WRAPPER=/usr/libexec/gcc/aarch64-linux-gnu/14/lto-wrapper OFFLOAD_TARGET_NAMES=nvptx-none OFFLOAD_TARGET_DEFAULT=1 Target: aarch64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 14.2.0-8' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=aarch64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libquadmath --disable-libquadmath-support --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --enable-fix-cortex-a53-843419 --disable-werror --enable-offload-targets=nvptx-none=/build/reproducible-path/gcc-14-14.2.0/debian/tmp-nvptx/usr --enable-offload-defaulted --without-cuda-driver --enable-checking=release --build=aarch64-linux-gnu --host=aarch64-linux-gnu --target=aarch64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=2 Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 14.2.0 (Debian 14.2.0-8) warning: mdtraj/formats/dcd/dcdlib.pxd:12:12: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. warning: mdtraj/formats/dcd/dcdlib.pxd:12:16: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. warning: mdtraj/formats/dcd/dcdlib.pxd:12:20: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. performance hint: mdtraj/geometry/src/image_molecules.pxi:15:5: Exception check on 'make_whole' will always require the GIL to be acquired. Possible solutions: 1. Declare 'make_whole' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on 'make_whole' to allow an error code to be returned. performance hint: mdtraj/geometry/src/image_molecules.pxi:36:5: Exception check on 'anchor_dists' will always require the GIL to be acquired. Possible solutions: 1. Declare 'anchor_dists' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on 'anchor_dists' to allow an error code to be returned. performance hint: mdtraj/geometry/src/image_molecules.pxi:68:5: Exception check on 'wrap_mols' will always require the GIL to be acquired. Possible solutions: 1. Declare 'wrap_mols' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on 'wrap_mols' to allow an error code to be returned. C compiler: Attempting to autodetect OpenMP support... Compiler supports OpenMP Attempting to autodetect SSE2 support... Did not detect SSE2 support Attempting to autodetect SSE3 support... Did not detect SSE3 support Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support Attempting to autodetect NEON support... Compiler supports NEON [ 1/10] Cythonizing mdtraj/formats/dcd/dcd.pyx [ 2/10] Cythonizing mdtraj/formats/dtr/dtr.pyx [ 3/10] Cythonizing mdtraj/formats/xtc/trr.pyx [ 4/10] Cythonizing mdtraj/formats/xtc/xtc.pyx [ 5/10] Cythonizing mdtraj/geometry/drid.pyx [ 6/10] Cythonizing mdtraj/geometry/neighborlist.pyx [ 7/10] Cythonizing mdtraj/geometry/neighbors.pyx [ 8/10] Cythonizing mdtraj/geometry/src/_geometry.pyx [ 9/10] Cythonizing mdtraj/rmsd/_lprmsd.pyx [10/10] Cythonizing mdtraj/rmsd/_rmsd.pyx running build running build_py creating /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj copying mdtraj/io.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj copying mdtraj/_version.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj copying mdtraj/__init__.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj creating /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils copying mdtraj/utils/zipped.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils copying mdtraj/utils/validation.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils copying mdtraj/utils/unitcell.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils copying mdtraj/utils/singleton.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils copying mdtraj/utils/rotation.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils copying mdtraj/utils/delay_import.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils copying mdtraj/utils/contextmanagers.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils copying mdtraj/utils/__init__.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils creating /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing copying mdtraj/testing/testing.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing copying mdtraj/testing/docstrings.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing copying mdtraj/testing/docscrape.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing copying mdtraj/testing/__init__.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing creating /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/scripts copying mdtraj/scripts/mdinspect.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/scripts copying mdtraj/scripts/mdconvert.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/scripts copying mdtraj/scripts/__init__.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/scripts creating /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/xtcreporter.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/netcdfreporter.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/hdf5reporter.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/dcdreporter.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/basereporter.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/__init__.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters creating /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/nmr copying mdtraj/nmr/shift_wrappers.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/nmr copying mdtraj/nmr/scalar_couplings.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/nmr copying mdtraj/nmr/__init__.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/nmr creating /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/thermodynamic_properties.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/shape.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/sasa.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/rg.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/rdf.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/order.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/internal.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/hbond.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/dssp.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/distance.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/dihedral.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/contact.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/angle.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/alignment.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/__init__.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry creating /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/xyzfile.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/registry.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/psf.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/prmtop.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/pdbx.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/openmmxml.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/netcdf.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/mol2.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/mdcrd.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/lh5.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/lammpstrj.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/hoomdxml.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/hdf5.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/gsd.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/gro.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/arc.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/amberrst.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/__init__.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats creating /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core copying mdtraj/core/trajectory.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core copying mdtraj/core/topology.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core copying mdtraj/core/selection.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core copying mdtraj/core/residue_names.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core copying mdtraj/core/element.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core copying mdtraj/core/__init__.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core creating /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/unit.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/doctests.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/baseunit.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/basedimension.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/unit_operators.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/unit_math.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/unit_definitions.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/standard_dimensions.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/quantity.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/prefix.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/constants.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/mymatrix.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/__init__.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit creating /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb copying mdtraj/formats/pdb/pdbstructure.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb copying mdtraj/formats/pdb/pdbfile.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb copying mdtraj/formats/pdb/__init__.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb creating /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb/data copying mdtraj/formats/pdb/data/residues.xml -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb/data copying mdtraj/formats/pdb/data/pdbNames.xml -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb/data UPDATING /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/_version.py set /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/_version.py to '1.10.1' running build_ext building 'mdtraj.formats.xtc' extension creating build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/src aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/src/xdrfile.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_decompress_coord_float': mdtraj/formats/xtc/src/xdrfile.c:788:32: warning: variable 'larger' set but not used [-Wunused-but-set-variable] 788 | int smallnum, smaller, larger, i, is_smaller, run; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c:785:23: warning: variable 'minidx' set but not used [-Wunused-but-set-variable] 785 | int smallidx, minidx, maxidx; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_compress_coord_float': mdtraj/formats/xtc/src/xdrfile.c:1016:13: warning: variable 'errval' set but not used [-Wunused-but-set-variable] 1016 | int errval=1; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_decompress_coord_double': mdtraj/formats/xtc/src/xdrfile.c:1305:32: warning: variable 'larger' set but not used [-Wunused-but-set-variable] 1305 | int smallnum, smaller, larger, i, is_smaller, run; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c:1302:23: warning: variable 'minidx' set but not used [-Wunused-but-set-variable] 1302 | int smallidx, minidx, maxidx; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_compress_coord_double': mdtraj/formats/xtc/src/xdrfile.c:1509:13: warning: variable 'errval' set but not used [-Wunused-but-set-variable] 1509 | int errval=1; | ^~~~~~ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/xtc/src/xdrfile_xtc.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/src/xdrfile_xtc.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/formats/xtc/src/xdrfile_xtc.c: In function 'xtc_coord': mdtraj/formats/xtc/src/xdrfile_xtc.c:66:15: warning: unused variable 'j' [-Wunused-variable] 66 | int i,j,result; | ^ mdtraj/formats/xtc/src/xdrfile_xtc.c:66:13: warning: unused variable 'i' [-Wunused-variable] 66 | int i,j,result; | ^ mdtraj/formats/xtc/src/xdrfile_xtc.c: In function 'read_xtc_nframes': mdtraj/formats/xtc/src/xdrfile_xtc.c:119:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 119 | if (NULL == xd) | ^~ mdtraj/formats/xtc/src/xdrfile_xtc.c:122:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 122 | do { | ^~ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/xtc/xtc.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/xtc.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/formats/xtc/xtc.c:1263: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ In function '__Pyx_PyInt_From_int', inlined from '__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_16_write' at mdtraj/formats/xtc/xtc.c:13728:16, inlined from '__pyx_pw_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_17_write' at mdtraj/formats/xtc/xtc.c:13424:13: mdtraj/formats/xtc/xtc.c:1165:40: warning: '__pyx_v_status' may be used uninitialized [-Wmaybe-uninitialized] 1165 | #define PyInt_FromLong PyLong_FromLong | ^ mdtraj/formats/xtc/xtc.c:25481:20: note: in expansion of macro 'PyInt_FromLong' 25481 | return PyInt_FromLong((long) value); | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c: In function '__pyx_pw_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_17_write': mdtraj/formats/xtc/xtc.c:13444:7: note: '__pyx_v_status' was declared here 13444 | int __pyx_v_status; | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c: In function '__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_12_read': mdtraj/formats/xtc/xtc.c:11491:10: warning: '__pyx_pybuffernd_framebuffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 11491 | if (unlikely(__pyx_t_5 != -1)) { | ^ mdtraj/formats/xtc/xtc.c:10279:21: note: '__pyx_pybuffernd_framebuffer.diminfo[0].shape' was declared here 10279 | __Pyx_LocalBuf_ND __pyx_pybuffernd_framebuffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:11490:17: warning: '__pyx_pybuffernd_framebuffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 11490 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_framebuffer.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/xtc.c:10279:21: note: '__pyx_pybuffernd_framebuffer.diminfo[1].shape' was declared here 10279 | __Pyx_LocalBuf_ND __pyx_pybuffernd_framebuffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:11856:23: warning: '__pyx_pybuffernd_box_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 11856 | } else if (unlikely(__pyx_t_33 >= __pyx_pybuffernd_box_stride.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/xtc.c:10277:21: note: '__pyx_pybuffernd_box_stride.diminfo[0].shape' was declared here 10277 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:11860:23: warning: '__pyx_pybuffernd_box_stride.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 11860 | } else if (unlikely(__pyx_t_34 >= __pyx_pybuffernd_box_stride.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/xtc.c:10277:21: note: '__pyx_pybuffernd_box_stride.diminfo[1].shape' was declared here 10277 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:11864:23: warning: '__pyx_pybuffernd_box_stride.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 11864 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_box_stride.diminfo[2].shape)) __pyx_t_5 = 2; | ^ mdtraj/formats/xtc/xtc.c:10277:21: note: '__pyx_pybuffernd_box_stride.diminfo[2].shape' was declared here 10277 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:11902:23: warning: '__pyx_pybuffernd_prec_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 11902 | } else if (unlikely(__pyx_t_41 >= __pyx_pybuffernd_prec_stride.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/xtc.c:10283:21: note: '__pyx_pybuffernd_prec_stride.diminfo[0].shape' was declared here 10283 | __Pyx_LocalBuf_ND __pyx_pybuffernd_prec_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:11826:23: warning: '__pyx_pybuffernd_step_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 11826 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_step_stride.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/xtc.c:10287:21: note: '__pyx_pybuffernd_step_stride.diminfo[0].shape' was declared here 10287 | __Pyx_LocalBuf_ND __pyx_pybuffernd_step_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:11844:23: warning: '__pyx_pybuffernd_time_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 11844 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_time_stride.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/xtc.c:10291:21: note: '__pyx_pybuffernd_time_stride.diminfo[0].shape' was declared here 10291 | __Pyx_LocalBuf_ND __pyx_pybuffernd_time_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:11884:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 11884 | } else if (unlikely(__pyx_t_38 >= __pyx_pybuffernd_xyz_stride.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/xtc.c:10295:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[0].shape' was declared here 10295 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:11888:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 11888 | } else if (unlikely(__pyx_t_39 >= __pyx_pybuffernd_xyz_stride.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/xtc.c:10295:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[1].shape' was declared here 10295 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:11892:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 11892 | } else if (unlikely(__pyx_t_40 >= __pyx_pybuffernd_xyz_stride.diminfo[2].shape)) __pyx_t_5 = 2; | ^ mdtraj/formats/xtc/xtc.c:10295:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[2].shape' was declared here 10295 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/src/xdrfile_xtc.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/xtc.o -L/usr/lib/aarch64-linux-gnu -o /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/xtc.cpython-312-aarch64-linux-gnu.so building 'mdtraj.formats.trr' extension aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/src/xdrfile.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_decompress_coord_float': mdtraj/formats/xtc/src/xdrfile.c:788:32: warning: variable 'larger' set but not used [-Wunused-but-set-variable] 788 | int smallnum, smaller, larger, i, is_smaller, run; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c:785:23: warning: variable 'minidx' set but not used [-Wunused-but-set-variable] 785 | int smallidx, minidx, maxidx; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_compress_coord_float': mdtraj/formats/xtc/src/xdrfile.c:1016:13: warning: variable 'errval' set but not used [-Wunused-but-set-variable] 1016 | int errval=1; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_decompress_coord_double': mdtraj/formats/xtc/src/xdrfile.c:1305:32: warning: variable 'larger' set but not used [-Wunused-but-set-variable] 1305 | int smallnum, smaller, larger, i, is_smaller, run; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c:1302:23: warning: variable 'minidx' set but not used [-Wunused-but-set-variable] 1302 | int smallidx, minidx, maxidx; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_compress_coord_double': mdtraj/formats/xtc/src/xdrfile.c:1509:13: warning: variable 'errval' set but not used [-Wunused-but-set-variable] 1509 | int errval=1; | ^~~~~~ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/xtc/src/xdrfile_trr.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/src/xdrfile_trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/xtc/trr.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/formats/xtc/trr.c:1265: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ In function '__Pyx_PyInt_From_int', inlined from '__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_18_write' at mdtraj/formats/xtc/trr.c:15643:16, inlined from '__pyx_pw_6mdtraj_7formats_3trr_17TRRTrajectoryFile_19_write' at mdtraj/formats/xtc/trr.c:15083:13: mdtraj/formats/xtc/trr.c:1167:40: warning: '__pyx_v_status' may be used uninitialized [-Wmaybe-uninitialized] 1167 | #define PyInt_FromLong PyLong_FromLong | ^ mdtraj/formats/xtc/trr.c:27476:20: note: in expansion of macro 'PyInt_FromLong' 27476 | return PyInt_FromLong((long) value); | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c: In function '__pyx_pw_6mdtraj_7formats_3trr_17TRRTrajectoryFile_19_write': mdtraj/formats/xtc/trr.c:15111:7: note: '__pyx_v_status' was declared here 15111 | int __pyx_v_status; | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c: In function '__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_14_read': mdtraj/formats/xtc/trr.c:12632:12: warning: '__pyx_pybuffernd_forces_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 12632 | if (unlikely(__pyx_t_4 != -1)) { | ^ mdtraj/formats/xtc/trr.c:10939:21: note: '__pyx_pybuffernd_forces_buffer.diminfo[0].shape' was declared here 10939 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:12631:19: warning: '__pyx_pybuffernd_forces_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 12631 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_forces_buffer.diminfo[1].shape)) __pyx_t_4 = 1; | ^ mdtraj/formats/xtc/trr.c:10939:21: note: '__pyx_pybuffernd_forces_buffer.diminfo[1].shape' was declared here 10939 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:12580:12: warning: '__pyx_pybuffernd_vel_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 12580 | if (unlikely(__pyx_t_4 != -1)) { | ^ mdtraj/formats/xtc/trr.c:10955:21: note: '__pyx_pybuffernd_vel_buffer.diminfo[0].shape' was declared here 10955 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:12579:19: warning: '__pyx_pybuffernd_vel_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 12579 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_vel_buffer.diminfo[1].shape)) __pyx_t_4 = 1; | ^ mdtraj/formats/xtc/trr.c:10955:21: note: '__pyx_pybuffernd_vel_buffer.diminfo[1].shape' was declared here 10955 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:12739:10: warning: '__pyx_pybuffernd_xyz_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 12739 | if (unlikely(__pyx_t_4 != -1)) { | ^ mdtraj/formats/xtc/trr.c:10959:21: note: '__pyx_pybuffernd_xyz_buffer.diminfo[0].shape' was declared here 10959 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:12738:17: warning: '__pyx_pybuffernd_xyz_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 12738 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_xyz_buffer.diminfo[1].shape)) __pyx_t_4 = 1; | ^ mdtraj/formats/xtc/trr.c:10959:21: note: '__pyx_pybuffernd_xyz_buffer.diminfo[1].shape' was declared here 10959 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:12341:19: warning: '__pyx_pybuffernd_vel.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 12341 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_vel.diminfo[0].shape)) __pyx_t_4 = 0; | ^ mdtraj/formats/xtc/trr.c:10953:21: note: '__pyx_pybuffernd_vel.diminfo[0].shape' was declared here 10953 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:2533:90: warning: '__pyx_pybuffernd_vel.diminfo[0].strides' may be used uninitialized [-Wmaybe-uninitialized] 2533 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) | ^ mdtraj/formats/xtc/trr.c:12354:42: note: in expansion of macro '__Pyx_BufPtrCContig3d' 12354 | __pyx_v_frame_vel = ((rvec *)(&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_vel.rcbuffer->pybuffer.buf, __pyx_t_29, __pyx_pybuffernd_vel.diminfo[0].strides, __pyx_t_30, __pyx_pybuffernd_vel.diminfo[1].strides, __pyx_t_31, __pyx_pybuffernd_vel.diminfo[2].strides)))); | ^~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:10953:21: note: '__pyx_pybuffernd_vel.diminfo[0].strides' was declared here 10953 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:12345:19: warning: '__pyx_pybuffernd_vel.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 12345 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_vel.diminfo[1].shape)) __pyx_t_4 = 1; | ^ mdtraj/formats/xtc/trr.c:10953:21: note: '__pyx_pybuffernd_vel.diminfo[1].shape' was declared here 10953 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:12349:19: warning: '__pyx_pybuffernd_vel.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 12349 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_vel.diminfo[2].shape)) __pyx_t_4 = 2; | ^ mdtraj/formats/xtc/trr.c:10953:21: note: '__pyx_pybuffernd_vel.diminfo[2].shape' was declared here 10953 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:12398:19: warning: '__pyx_pybuffernd_forces.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 12398 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_forces.diminfo[0].shape)) __pyx_t_4 = 0; | ^ mdtraj/formats/xtc/trr.c:10937:21: note: '__pyx_pybuffernd_forces.diminfo[0].shape' was declared here 10937 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:2533:90: warning: '__pyx_pybuffernd_forces.diminfo[0].strides' may be used uninitialized [-Wmaybe-uninitialized] 2533 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) | ^ mdtraj/formats/xtc/trr.c:12411:45: note: in expansion of macro '__Pyx_BufPtrCContig3d' 12411 | __pyx_v_frame_forces = ((rvec *)(&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_forces.rcbuffer->pybuffer.buf, __pyx_t_29, __pyx_pybuffernd_forces.diminfo[0].strides, __pyx_t_31, __pyx_pybuffernd_forces.diminfo[1].strides, __pyx_t_30, __pyx_pybuffernd_forces.diminfo[2].strides)))); | ^~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:10937:21: note: '__pyx_pybuffernd_forces.diminfo[0].strides' was declared here 10937 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:12402:19: warning: '__pyx_pybuffernd_forces.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 12402 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_forces.diminfo[1].shape)) __pyx_t_4 = 1; | ^ mdtraj/formats/xtc/trr.c:10937:21: note: '__pyx_pybuffernd_forces.diminfo[1].shape' was declared here 10937 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:12406:19: warning: '__pyx_pybuffernd_forces.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 12406 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_forces.diminfo[2].shape)) __pyx_t_4 = 2; | ^ mdtraj/formats/xtc/trr.c:10937:21: note: '__pyx_pybuffernd_forces.diminfo[2].shape' was declared here 10937 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/src/xdrfile_trr.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/trr.o -L/usr/lib/aarch64-linux-gnu -o /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/trr.cpython-312-aarch64-linux-gnu.so building 'mdtraj.formats.dcd' extension creating build/temp.linux-aarch64-cpython-312/mdtraj/formats/dcd creating build/temp.linux-aarch64-cpython-312/mdtraj/formats/dcd/src aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/dcd -Imdtraj/formats/dcd/include/ -Imdtraj/formats/dcd/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/dcd/dcd.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/dcd/dcd.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/formats/dcd/dcd.c:1260: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ In function '__Pyx_PyInt_From_int', inlined from '__pyx_pf_6mdtraj_7formats_3dcd_17DCDTrajectoryFile_20read' at mdtraj/formats/dcd/dcd.c:10190:17: mdtraj/formats/dcd/dcd.c:1162:40: warning: '__pyx_v_i' may be used uninitialized [-Wmaybe-uninitialized] 1162 | #define PyInt_FromLong PyLong_FromLong | ^ mdtraj/formats/dcd/dcd.c:18997:20: note: in expansion of macro 'PyInt_FromLong' 18997 | return PyInt_FromLong((long) value); | ^~~~~~~~~~~~~~ mdtraj/formats/dcd/dcd.c: In function '__pyx_pf_6mdtraj_7formats_3dcd_17DCDTrajectoryFile_20read': mdtraj/formats/dcd/dcd.c:8994:7: note: '__pyx_v_i' was declared here 8994 | int __pyx_v_i; | ^~~~~~~~~ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/dcd -Imdtraj/formats/dcd/include/ -Imdtraj/formats/dcd/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/dcd/src/dcdplugin.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/dcd/src/dcdplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/mdtraj/formats/dcd/dcd.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/dcd/src/dcdplugin.o -L/usr/lib/aarch64-linux-gnu -o /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/dcd.cpython-312-aarch64-linux-gnu.so building 'mdtraj.formats.dtr' extension creating build/temp.linux-aarch64-cpython-312/mdtraj/formats/dtr creating build/temp.linux-aarch64-cpython-312/mdtraj/formats/dtr/src aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/dtr/dtr.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/dtr/dtr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/formats/dtr/dtr.cpp:1279: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/dtr/src/dtrplugin.cxx -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/dtr/src/dtrplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/formats/dtr/src/dtrplugin.cxx: In member function 'bool desres::molfile::Timekeys::init(const std::string&)': mdtraj/formats/dtr/src/dtrplugin.cxx:487:27: warning: format '%d' expects argument of type 'int', but argument 2 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] 487 | printf("size %d framesize %d\n\n", | ~^ | | | int | %ld 488 | keys[i].size(), m_framesize); | ~~~~~~~~~~~~~~ | | | uint64_t {aka long unsigned int} mdtraj/formats/dtr/src/dtrplugin.cxx:487:40: warning: format '%d' expects argument of type 'int', but argument 3 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] 487 | printf("size %d framesize %d\n\n", | ~^ | | | int | %ld 488 | keys[i].size(), m_framesize); | ~~~~~~~~~~~ | | | uint64_t {aka long unsigned int} mdtraj/formats/dtr/src/dtrplugin.cxx: In function 'void DDmkdir(const std::string&, mode_t, int, int)': mdtraj/formats/dtr/src/dtrplugin.cxx:706:23: warning: '%03x' directive writing between 3 and 8 bytes into a region of size 6 [-Wformat-overflow=] 706 | sprintf(sub, "%03x/", i); | ^~~~ mdtraj/formats/dtr/src/dtrplugin.cxx:706:22: note: directive argument in the range [0, 2147483646] 706 | sprintf(sub, "%03x/", i); | ^~~~~~~ In file included from /usr/include/stdio.h:970, from mdtraj/formats/dtr/include/molfile_plugin.h:35, from mdtraj/formats/dtr/include/dtrplugin.hxx:46, from mdtraj/formats/dtr/src/dtrplugin.cxx:42: In function 'int sprintf(char*, const char*, ...)', inlined from 'void DDmkdir(const std::string&, mode_t, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:706:9: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 5 and 10 bytes into a destination of size 6 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ mdtraj/formats/dtr/src/dtrplugin.cxx: In function 'void DDmkdir(const std::string&, mode_t, int, int)': mdtraj/formats/dtr/src/dtrplugin.cxx:714:30: warning: '%03x' directive writing between 3 and 8 bytes into a region of size 6 [-Wformat-overflow=] 714 | sprintf(subsub, "%03x", j); | ^~~~ mdtraj/formats/dtr/src/dtrplugin.cxx:714:29: note: directive argument in the range [0, 2147483646] 714 | sprintf(subsub, "%03x", j); | ^~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'void DDmkdir(const std::string&, mode_t, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:714:13: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 4 and 9 bytes into a destination of size 6 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ mdtraj/formats/dtr/src/dtrplugin.cxx: In function 'std::string framefile(const std::string&, size_t, size_t, int, int)': mdtraj/formats/dtr/src/dtrplugin.cxx:667:35: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=] 667 | sprintf(answer, "%03x/", d1); | ^ In function 'int sprintf(char*, const char*, ...)', inlined from 'std::string DDreldir(const std::string&, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:667:13, inlined from 'std::string framefile(const std::string&, size_t, size_t, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:771:23: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 5 and 10 bytes into a destination of size 9 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ mdtraj/formats/dtr/src/dtrplugin.cxx: In function 'std::string framefile(const std::string&, size_t, size_t, int, int)': mdtraj/formats/dtr/src/dtrplugin.cxx:665:35: warning: '%03x' directive writing between 3 and 8 bytes into a region of size between 0 and 5 [-Wformat-overflow=] 665 | sprintf(answer, "%03x/%03x/", d1, d2); | ^~~~ In function 'std::string DDreldir(const std::string&, int, int)', inlined from 'std::string framefile(const std::string&, size_t, size_t, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:771:23: mdtraj/formats/dtr/src/dtrplugin.cxx:665:29: note: directive argument in the range [0, 2147483646] 665 | sprintf(answer, "%03x/%03x/", d1, d2); | ^~~~~~~~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'std::string DDreldir(const std::string&, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:665:13, inlined from 'std::string framefile(const std::string&, size_t, size_t, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:771:23: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 9 and 19 bytes into a destination of size 9 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/mdtraj/formats/dtr/dtr.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/dtr/src/dtrplugin.o -L/usr/lib/aarch64-linux-gnu -o /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/dtr.cpython-312-aarch64-linux-gnu.so building 'mdtraj._rmsd' extension creating build/temp.linux-aarch64-cpython-312/mdtraj/rmsd creating build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/_rmsd.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/_rmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/center.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/rotation.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/rotation.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/theobald_rmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/_rmsd.o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/center.o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/rotation.o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/_rmsd.cpython-312-aarch64-linux-gnu.so building 'mdtraj._lprmsd' extension aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/_lprmsd.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/_lprmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/rmsd/_lprmsd.cpp:1305: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/Munkres.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/Munkres.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/center.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/euclidean_permutation.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/euclidean_permutation.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/fancy_index.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/fancy_index.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/rotation.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/rotation.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/theobald_rmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/_lprmsd.o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/Munkres.o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/center.o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/euclidean_permutation.o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/fancy_index.o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/rotation.o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/_lprmsd.cpython-312-aarch64-linux-gnu.so building 'mdtraj.core.lib.libtheobald' extension aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/theobald_rmsd.o -O3 -funroll-loops --std=c++11 aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/center.o -O3 -funroll-loops --std=c++11 aarch64-linux-gnu-gcc-ar rcs /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/lib/libtheobald.a build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/theobald_rmsd.o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/center.o building 'mdtraj.geometry._geometry' extension creating build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/src/_geometry.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/_geometry.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/geometry/src/_geometry.cpp:1287: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/src/dssp.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/dssp.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/src/geometry.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/geometry.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/src/sasa.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/sasa.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/_geometry.o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/dssp.o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/geometry.o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/sasa.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/_geometry.cpython-312-aarch64-linux-gnu.so building 'mdtraj.geometry.drid' extension aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/drid.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/drid.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/src/dridkernels.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/dridkernels.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/src/moments.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/moments.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/mdtraj/geometry/drid.o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/dridkernels.o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/moments.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/drid.cpython-312-aarch64-linux-gnu.so building 'mdtraj.geometry.neighbors' extension aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/neighbors.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/neighbors.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/src/neighbors.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/neighbors.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/mdtraj/geometry/neighbors.o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/neighbors.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/neighbors.cpython-312-aarch64-linux-gnu.so building 'mdtraj.geometry.neighborlist' extension aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/neighborlist.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/neighborlist.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/src/neighborlist.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/neighborlist.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/mdtraj/geometry/neighborlist.o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/neighborlist.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/neighborlist.cpython-312-aarch64-linux-gnu.so dh_auto_test -O--buildsystem=pybuild pybuild --test -i python{version} -p 3.12 I: pybuild base:311: cd /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build; python3.12 -m unittest discover -v ---------------------------------------------------------------------- Ran 0 tests in 0.000s NO TESTS RAN rm -fr -- /tmp/dh-xdg-rundir-ixZqDP7V create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild rm -f -- debian/python3-mdtraj.substvars debian/python-mdtraj-doc.substvars rm -fr -- debian/.debhelper/generated/python3-mdtraj/ debian/python3-mdtraj/ debian/tmp/ debian/.debhelper/generated/python-mdtraj-doc/ debian/python-mdtraj-doc/ dh_installdirs -O--buildsystem=pybuild install -m0755 -d debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples/data dh_auto_install -O--buildsystem=pybuild install -m0755 -d /build/reproducible-path/mdtraj-1.10.1/debian/tmp pybuild --install -i python{version} -p 3.12 --dest-dir /build/reproducible-path/mdtraj-1.10.1/debian/tmp I: pybuild base:311: /usr/bin/python3 setup.py install --root /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj Using built-in specs. COLLECT_GCC=/usr/bin/aarch64-linux-gnu-gcc COLLECT_LTO_WRAPPER=/usr/libexec/gcc/aarch64-linux-gnu/14/lto-wrapper OFFLOAD_TARGET_NAMES=nvptx-none OFFLOAD_TARGET_DEFAULT=1 Target: aarch64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 14.2.0-8' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=aarch64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libquadmath --disable-libquadmath-support --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --enable-fix-cortex-a53-843419 --disable-werror --enable-offload-targets=nvptx-none=/build/reproducible-path/gcc-14-14.2.0/debian/tmp-nvptx/usr --enable-offload-defaulted --without-cuda-driver --enable-checking=release --build=aarch64-linux-gnu --host=aarch64-linux-gnu --target=aarch64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=2 Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 14.2.0 (Debian 14.2.0-8) warning: mdtraj/formats/dcd/dcdlib.pxd:12:12: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. warning: mdtraj/formats/dcd/dcdlib.pxd:12:16: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. warning: mdtraj/formats/dcd/dcdlib.pxd:12:20: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. performance hint: mdtraj/geometry/src/image_molecules.pxi:15:5: Exception check on 'make_whole' will always require the GIL to be acquired. Possible solutions: 1. Declare 'make_whole' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on 'make_whole' to allow an error code to be returned. performance hint: mdtraj/geometry/src/image_molecules.pxi:36:5: Exception check on 'anchor_dists' will always require the GIL to be acquired. Possible solutions: 1. Declare 'anchor_dists' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on 'anchor_dists' to allow an error code to be returned. performance hint: mdtraj/geometry/src/image_molecules.pxi:68:5: Exception check on 'wrap_mols' will always require the GIL to be acquired. Possible solutions: 1. Declare 'wrap_mols' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on 'wrap_mols' to allow an error code to be returned. C compiler: Attempting to autodetect OpenMP support... Compiler supports OpenMP Attempting to autodetect SSE2 support... Did not detect SSE2 support Attempting to autodetect SSE3 support... Did not detect SSE3 support Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support Attempting to autodetect NEON support... Compiler supports NEON [ 1/10] Cythonizing mdtraj/formats/dcd/dcd.pyx [ 2/10] Cythonizing mdtraj/formats/dtr/dtr.pyx [ 3/10] Cythonizing mdtraj/formats/xtc/trr.pyx [ 4/10] Cythonizing mdtraj/formats/xtc/xtc.pyx [ 5/10] Cythonizing mdtraj/geometry/drid.pyx [ 6/10] Cythonizing mdtraj/geometry/neighborlist.pyx [ 7/10] Cythonizing mdtraj/geometry/neighbors.pyx [ 8/10] Cythonizing mdtraj/geometry/src/_geometry.pyx [ 9/10] Cythonizing mdtraj/rmsd/_lprmsd.pyx [10/10] Cythonizing mdtraj/rmsd/_rmsd.pyx running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running build running build_py UPDATING /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/_version.py set /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/_version.py to '1.10.1' running build_ext building 'mdtraj.formats.xtc' extension aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/src/xdrfile.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_decompress_coord_float': mdtraj/formats/xtc/src/xdrfile.c:788:32: warning: variable 'larger' set but not used [-Wunused-but-set-variable] 788 | int smallnum, smaller, larger, i, is_smaller, run; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c:785:23: warning: variable 'minidx' set but not used [-Wunused-but-set-variable] 785 | int smallidx, minidx, maxidx; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_compress_coord_float': mdtraj/formats/xtc/src/xdrfile.c:1016:13: warning: variable 'errval' set but not used [-Wunused-but-set-variable] 1016 | int errval=1; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_decompress_coord_double': mdtraj/formats/xtc/src/xdrfile.c:1305:32: warning: variable 'larger' set but not used [-Wunused-but-set-variable] 1305 | int smallnum, smaller, larger, i, is_smaller, run; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c:1302:23: warning: variable 'minidx' set but not used [-Wunused-but-set-variable] 1302 | int smallidx, minidx, maxidx; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_compress_coord_double': mdtraj/formats/xtc/src/xdrfile.c:1509:13: warning: variable 'errval' set but not used [-Wunused-but-set-variable] 1509 | int errval=1; | ^~~~~~ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/xtc/src/xdrfile_xtc.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/src/xdrfile_xtc.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/formats/xtc/src/xdrfile_xtc.c: In function 'xtc_coord': mdtraj/formats/xtc/src/xdrfile_xtc.c:66:15: warning: unused variable 'j' [-Wunused-variable] 66 | int i,j,result; | ^ mdtraj/formats/xtc/src/xdrfile_xtc.c:66:13: warning: unused variable 'i' [-Wunused-variable] 66 | int i,j,result; | ^ mdtraj/formats/xtc/src/xdrfile_xtc.c: In function 'read_xtc_nframes': mdtraj/formats/xtc/src/xdrfile_xtc.c:119:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 119 | if (NULL == xd) | ^~ mdtraj/formats/xtc/src/xdrfile_xtc.c:122:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 122 | do { | ^~ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/xtc/xtc.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/xtc.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/formats/xtc/xtc.c:1263: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ In function '__Pyx_PyInt_From_int', inlined from '__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_16_write' at mdtraj/formats/xtc/xtc.c:13728:16, inlined from '__pyx_pw_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_17_write' at mdtraj/formats/xtc/xtc.c:13424:13: mdtraj/formats/xtc/xtc.c:1165:40: warning: '__pyx_v_status' may be used uninitialized [-Wmaybe-uninitialized] 1165 | #define PyInt_FromLong PyLong_FromLong | ^ mdtraj/formats/xtc/xtc.c:25481:20: note: in expansion of macro 'PyInt_FromLong' 25481 | return PyInt_FromLong((long) value); | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c: In function '__pyx_pw_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_17_write': mdtraj/formats/xtc/xtc.c:13444:7: note: '__pyx_v_status' was declared here 13444 | int __pyx_v_status; | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c: In function '__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_12_read': mdtraj/formats/xtc/xtc.c:11491:10: warning: '__pyx_pybuffernd_framebuffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 11491 | if (unlikely(__pyx_t_5 != -1)) { | ^ mdtraj/formats/xtc/xtc.c:10279:21: note: '__pyx_pybuffernd_framebuffer.diminfo[0].shape' was declared here 10279 | __Pyx_LocalBuf_ND __pyx_pybuffernd_framebuffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:11490:17: warning: '__pyx_pybuffernd_framebuffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 11490 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_framebuffer.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/xtc.c:10279:21: note: '__pyx_pybuffernd_framebuffer.diminfo[1].shape' was declared here 10279 | __Pyx_LocalBuf_ND __pyx_pybuffernd_framebuffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:11856:23: warning: '__pyx_pybuffernd_box_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 11856 | } else if (unlikely(__pyx_t_33 >= __pyx_pybuffernd_box_stride.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/xtc.c:10277:21: note: '__pyx_pybuffernd_box_stride.diminfo[0].shape' was declared here 10277 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:11860:23: warning: '__pyx_pybuffernd_box_stride.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 11860 | } else if (unlikely(__pyx_t_34 >= __pyx_pybuffernd_box_stride.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/xtc.c:10277:21: note: '__pyx_pybuffernd_box_stride.diminfo[1].shape' was declared here 10277 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:11864:23: warning: '__pyx_pybuffernd_box_stride.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 11864 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_box_stride.diminfo[2].shape)) __pyx_t_5 = 2; | ^ mdtraj/formats/xtc/xtc.c:10277:21: note: '__pyx_pybuffernd_box_stride.diminfo[2].shape' was declared here 10277 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:11902:23: warning: '__pyx_pybuffernd_prec_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 11902 | } else if (unlikely(__pyx_t_41 >= __pyx_pybuffernd_prec_stride.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/xtc.c:10283:21: note: '__pyx_pybuffernd_prec_stride.diminfo[0].shape' was declared here 10283 | __Pyx_LocalBuf_ND __pyx_pybuffernd_prec_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:11826:23: warning: '__pyx_pybuffernd_step_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 11826 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_step_stride.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/xtc.c:10287:21: note: '__pyx_pybuffernd_step_stride.diminfo[0].shape' was declared here 10287 | __Pyx_LocalBuf_ND __pyx_pybuffernd_step_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:11844:23: warning: '__pyx_pybuffernd_time_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 11844 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_time_stride.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/xtc.c:10291:21: note: '__pyx_pybuffernd_time_stride.diminfo[0].shape' was declared here 10291 | __Pyx_LocalBuf_ND __pyx_pybuffernd_time_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:11884:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 11884 | } else if (unlikely(__pyx_t_38 >= __pyx_pybuffernd_xyz_stride.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/xtc.c:10295:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[0].shape' was declared here 10295 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:11888:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 11888 | } else if (unlikely(__pyx_t_39 >= __pyx_pybuffernd_xyz_stride.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/xtc.c:10295:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[1].shape' was declared here 10295 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:11892:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 11892 | } else if (unlikely(__pyx_t_40 >= __pyx_pybuffernd_xyz_stride.diminfo[2].shape)) __pyx_t_5 = 2; | ^ mdtraj/formats/xtc/xtc.c:10295:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[2].shape' was declared here 10295 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/src/xdrfile_xtc.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/xtc.o -L/usr/lib/aarch64-linux-gnu -o /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/xtc.cpython-312-aarch64-linux-gnu.so building 'mdtraj.formats.trr' extension aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/src/xdrfile.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_decompress_coord_float': mdtraj/formats/xtc/src/xdrfile.c:788:32: warning: variable 'larger' set but not used [-Wunused-but-set-variable] 788 | int smallnum, smaller, larger, i, is_smaller, run; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c:785:23: warning: variable 'minidx' set but not used [-Wunused-but-set-variable] 785 | int smallidx, minidx, maxidx; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_compress_coord_float': mdtraj/formats/xtc/src/xdrfile.c:1016:13: warning: variable 'errval' set but not used [-Wunused-but-set-variable] 1016 | int errval=1; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_decompress_coord_double': mdtraj/formats/xtc/src/xdrfile.c:1305:32: warning: variable 'larger' set but not used [-Wunused-but-set-variable] 1305 | int smallnum, smaller, larger, i, is_smaller, run; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c:1302:23: warning: variable 'minidx' set but not used [-Wunused-but-set-variable] 1302 | int smallidx, minidx, maxidx; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_compress_coord_double': mdtraj/formats/xtc/src/xdrfile.c:1509:13: warning: variable 'errval' set but not used [-Wunused-but-set-variable] 1509 | int errval=1; | ^~~~~~ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/xtc/src/xdrfile_trr.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/src/xdrfile_trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/xtc/trr.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/formats/xtc/trr.c:1265: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ In function '__Pyx_PyInt_From_int', inlined from '__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_18_write' at mdtraj/formats/xtc/trr.c:15643:16, inlined from '__pyx_pw_6mdtraj_7formats_3trr_17TRRTrajectoryFile_19_write' at mdtraj/formats/xtc/trr.c:15083:13: mdtraj/formats/xtc/trr.c:1167:40: warning: '__pyx_v_status' may be used uninitialized [-Wmaybe-uninitialized] 1167 | #define PyInt_FromLong PyLong_FromLong | ^ mdtraj/formats/xtc/trr.c:27476:20: note: in expansion of macro 'PyInt_FromLong' 27476 | return PyInt_FromLong((long) value); | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c: In function '__pyx_pw_6mdtraj_7formats_3trr_17TRRTrajectoryFile_19_write': mdtraj/formats/xtc/trr.c:15111:7: note: '__pyx_v_status' was declared here 15111 | int __pyx_v_status; | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c: In function '__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_14_read': mdtraj/formats/xtc/trr.c:12632:12: warning: '__pyx_pybuffernd_forces_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 12632 | if (unlikely(__pyx_t_4 != -1)) { | ^ mdtraj/formats/xtc/trr.c:10939:21: note: '__pyx_pybuffernd_forces_buffer.diminfo[0].shape' was declared here 10939 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:12631:19: warning: '__pyx_pybuffernd_forces_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 12631 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_forces_buffer.diminfo[1].shape)) __pyx_t_4 = 1; | ^ mdtraj/formats/xtc/trr.c:10939:21: note: '__pyx_pybuffernd_forces_buffer.diminfo[1].shape' was declared here 10939 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:12580:12: warning: '__pyx_pybuffernd_vel_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 12580 | if (unlikely(__pyx_t_4 != -1)) { | ^ mdtraj/formats/xtc/trr.c:10955:21: note: '__pyx_pybuffernd_vel_buffer.diminfo[0].shape' was declared here 10955 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:12579:19: warning: '__pyx_pybuffernd_vel_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 12579 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_vel_buffer.diminfo[1].shape)) __pyx_t_4 = 1; | ^ mdtraj/formats/xtc/trr.c:10955:21: note: '__pyx_pybuffernd_vel_buffer.diminfo[1].shape' was declared here 10955 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:12739:10: warning: '__pyx_pybuffernd_xyz_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 12739 | if (unlikely(__pyx_t_4 != -1)) { | ^ mdtraj/formats/xtc/trr.c:10959:21: note: '__pyx_pybuffernd_xyz_buffer.diminfo[0].shape' was declared here 10959 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:12738:17: warning: '__pyx_pybuffernd_xyz_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 12738 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_xyz_buffer.diminfo[1].shape)) __pyx_t_4 = 1; | ^ mdtraj/formats/xtc/trr.c:10959:21: note: '__pyx_pybuffernd_xyz_buffer.diminfo[1].shape' was declared here 10959 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:12341:19: warning: '__pyx_pybuffernd_vel.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 12341 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_vel.diminfo[0].shape)) __pyx_t_4 = 0; | ^ mdtraj/formats/xtc/trr.c:10953:21: note: '__pyx_pybuffernd_vel.diminfo[0].shape' was declared here 10953 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:2533:90: warning: '__pyx_pybuffernd_vel.diminfo[0].strides' may be used uninitialized [-Wmaybe-uninitialized] 2533 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) | ^ mdtraj/formats/xtc/trr.c:12354:42: note: in expansion of macro '__Pyx_BufPtrCContig3d' 12354 | __pyx_v_frame_vel = ((rvec *)(&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_vel.rcbuffer->pybuffer.buf, __pyx_t_29, __pyx_pybuffernd_vel.diminfo[0].strides, __pyx_t_30, __pyx_pybuffernd_vel.diminfo[1].strides, __pyx_t_31, __pyx_pybuffernd_vel.diminfo[2].strides)))); | ^~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:10953:21: note: '__pyx_pybuffernd_vel.diminfo[0].strides' was declared here 10953 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:12345:19: warning: '__pyx_pybuffernd_vel.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 12345 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_vel.diminfo[1].shape)) __pyx_t_4 = 1; | ^ mdtraj/formats/xtc/trr.c:10953:21: note: '__pyx_pybuffernd_vel.diminfo[1].shape' was declared here 10953 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:12349:19: warning: '__pyx_pybuffernd_vel.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 12349 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_vel.diminfo[2].shape)) __pyx_t_4 = 2; | ^ mdtraj/formats/xtc/trr.c:10953:21: note: '__pyx_pybuffernd_vel.diminfo[2].shape' was declared here 10953 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:12398:19: warning: '__pyx_pybuffernd_forces.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 12398 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_forces.diminfo[0].shape)) __pyx_t_4 = 0; | ^ mdtraj/formats/xtc/trr.c:10937:21: note: '__pyx_pybuffernd_forces.diminfo[0].shape' was declared here 10937 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:2533:90: warning: '__pyx_pybuffernd_forces.diminfo[0].strides' may be used uninitialized [-Wmaybe-uninitialized] 2533 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) | ^ mdtraj/formats/xtc/trr.c:12411:45: note: in expansion of macro '__Pyx_BufPtrCContig3d' 12411 | __pyx_v_frame_forces = ((rvec *)(&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_forces.rcbuffer->pybuffer.buf, __pyx_t_29, __pyx_pybuffernd_forces.diminfo[0].strides, __pyx_t_31, __pyx_pybuffernd_forces.diminfo[1].strides, __pyx_t_30, __pyx_pybuffernd_forces.diminfo[2].strides)))); | ^~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:10937:21: note: '__pyx_pybuffernd_forces.diminfo[0].strides' was declared here 10937 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:12402:19: warning: '__pyx_pybuffernd_forces.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 12402 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_forces.diminfo[1].shape)) __pyx_t_4 = 1; | ^ mdtraj/formats/xtc/trr.c:10937:21: note: '__pyx_pybuffernd_forces.diminfo[1].shape' was declared here 10937 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:12406:19: warning: '__pyx_pybuffernd_forces.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 12406 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_forces.diminfo[2].shape)) __pyx_t_4 = 2; | ^ mdtraj/formats/xtc/trr.c:10937:21: note: '__pyx_pybuffernd_forces.diminfo[2].shape' was declared here 10937 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/src/xdrfile_trr.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/trr.o -L/usr/lib/aarch64-linux-gnu -o /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/trr.cpython-312-aarch64-linux-gnu.so building 'mdtraj.formats.dcd' extension aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/dcd -Imdtraj/formats/dcd/include/ -Imdtraj/formats/dcd/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/dcd/dcd.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/dcd/dcd.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/formats/dcd/dcd.c:1260: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ In function '__Pyx_PyInt_From_int', inlined from '__pyx_pf_6mdtraj_7formats_3dcd_17DCDTrajectoryFile_20read' at mdtraj/formats/dcd/dcd.c:10190:17: mdtraj/formats/dcd/dcd.c:1162:40: warning: '__pyx_v_i' may be used uninitialized [-Wmaybe-uninitialized] 1162 | #define PyInt_FromLong PyLong_FromLong | ^ mdtraj/formats/dcd/dcd.c:18997:20: note: in expansion of macro 'PyInt_FromLong' 18997 | return PyInt_FromLong((long) value); | ^~~~~~~~~~~~~~ mdtraj/formats/dcd/dcd.c: In function '__pyx_pf_6mdtraj_7formats_3dcd_17DCDTrajectoryFile_20read': mdtraj/formats/dcd/dcd.c:8994:7: note: '__pyx_v_i' was declared here 8994 | int __pyx_v_i; | ^~~~~~~~~ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/dcd -Imdtraj/formats/dcd/include/ -Imdtraj/formats/dcd/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/dcd/src/dcdplugin.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/dcd/src/dcdplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/mdtraj/formats/dcd/dcd.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/dcd/src/dcdplugin.o -L/usr/lib/aarch64-linux-gnu -o /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/dcd.cpython-312-aarch64-linux-gnu.so building 'mdtraj.formats.dtr' extension aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/dtr/dtr.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/dtr/dtr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/formats/dtr/dtr.cpp:1279: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/dtr/src/dtrplugin.cxx -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/dtr/src/dtrplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/formats/dtr/src/dtrplugin.cxx: In member function 'bool desres::molfile::Timekeys::init(const std::string&)': mdtraj/formats/dtr/src/dtrplugin.cxx:487:27: warning: format '%d' expects argument of type 'int', but argument 2 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] 487 | printf("size %d framesize %d\n\n", | ~^ | | | int | %ld 488 | keys[i].size(), m_framesize); | ~~~~~~~~~~~~~~ | | | uint64_t {aka long unsigned int} mdtraj/formats/dtr/src/dtrplugin.cxx:487:40: warning: format '%d' expects argument of type 'int', but argument 3 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] 487 | printf("size %d framesize %d\n\n", | ~^ | | | int | %ld 488 | keys[i].size(), m_framesize); | ~~~~~~~~~~~ | | | uint64_t {aka long unsigned int} mdtraj/formats/dtr/src/dtrplugin.cxx: In function 'void DDmkdir(const std::string&, mode_t, int, int)': mdtraj/formats/dtr/src/dtrplugin.cxx:706:23: warning: '%03x' directive writing between 3 and 8 bytes into a region of size 6 [-Wformat-overflow=] 706 | sprintf(sub, "%03x/", i); | ^~~~ mdtraj/formats/dtr/src/dtrplugin.cxx:706:22: note: directive argument in the range [0, 2147483646] 706 | sprintf(sub, "%03x/", i); | ^~~~~~~ In file included from /usr/include/stdio.h:970, from mdtraj/formats/dtr/include/molfile_plugin.h:35, from mdtraj/formats/dtr/include/dtrplugin.hxx:46, from mdtraj/formats/dtr/src/dtrplugin.cxx:42: In function 'int sprintf(char*, const char*, ...)', inlined from 'void DDmkdir(const std::string&, mode_t, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:706:9: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 5 and 10 bytes into a destination of size 6 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ mdtraj/formats/dtr/src/dtrplugin.cxx: In function 'void DDmkdir(const std::string&, mode_t, int, int)': mdtraj/formats/dtr/src/dtrplugin.cxx:714:30: warning: '%03x' directive writing between 3 and 8 bytes into a region of size 6 [-Wformat-overflow=] 714 | sprintf(subsub, "%03x", j); | ^~~~ mdtraj/formats/dtr/src/dtrplugin.cxx:714:29: note: directive argument in the range [0, 2147483646] 714 | sprintf(subsub, "%03x", j); | ^~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'void DDmkdir(const std::string&, mode_t, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:714:13: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 4 and 9 bytes into a destination of size 6 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ mdtraj/formats/dtr/src/dtrplugin.cxx: In function 'std::string framefile(const std::string&, size_t, size_t, int, int)': mdtraj/formats/dtr/src/dtrplugin.cxx:667:35: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=] 667 | sprintf(answer, "%03x/", d1); | ^ In function 'int sprintf(char*, const char*, ...)', inlined from 'std::string DDreldir(const std::string&, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:667:13, inlined from 'std::string framefile(const std::string&, size_t, size_t, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:771:23: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 5 and 10 bytes into a destination of size 9 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ mdtraj/formats/dtr/src/dtrplugin.cxx: In function 'std::string framefile(const std::string&, size_t, size_t, int, int)': mdtraj/formats/dtr/src/dtrplugin.cxx:665:35: warning: '%03x' directive writing between 3 and 8 bytes into a region of size between 0 and 5 [-Wformat-overflow=] 665 | sprintf(answer, "%03x/%03x/", d1, d2); | ^~~~ In function 'std::string DDreldir(const std::string&, int, int)', inlined from 'std::string framefile(const std::string&, size_t, size_t, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:771:23: mdtraj/formats/dtr/src/dtrplugin.cxx:665:29: note: directive argument in the range [0, 2147483646] 665 | sprintf(answer, "%03x/%03x/", d1, d2); | ^~~~~~~~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'std::string DDreldir(const std::string&, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:665:13, inlined from 'std::string framefile(const std::string&, size_t, size_t, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:771:23: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 9 and 19 bytes into a destination of size 9 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/mdtraj/formats/dtr/dtr.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/dtr/src/dtrplugin.o -L/usr/lib/aarch64-linux-gnu -o /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/dtr.cpython-312-aarch64-linux-gnu.so building 'mdtraj._rmsd' extension aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/_rmsd.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/_rmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/center.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/rotation.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/rotation.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/theobald_rmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/_rmsd.o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/center.o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/rotation.o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/_rmsd.cpython-312-aarch64-linux-gnu.so building 'mdtraj._lprmsd' extension aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/_lprmsd.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/_lprmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/rmsd/_lprmsd.cpp:1305: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/Munkres.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/Munkres.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/center.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/euclidean_permutation.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/euclidean_permutation.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/fancy_index.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/fancy_index.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/rotation.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/rotation.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/theobald_rmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/_lprmsd.o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/Munkres.o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/center.o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/euclidean_permutation.o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/fancy_index.o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/rotation.o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/_lprmsd.cpython-312-aarch64-linux-gnu.so building 'mdtraj.geometry._geometry' extension aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/src/_geometry.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/_geometry.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/geometry/src/_geometry.cpp:1287: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/src/dssp.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/dssp.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/src/geometry.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/geometry.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/src/sasa.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/sasa.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/_geometry.o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/dssp.o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/geometry.o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/sasa.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/_geometry.cpython-312-aarch64-linux-gnu.so building 'mdtraj.geometry.drid' extension aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/drid.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/drid.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/src/dridkernels.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/dridkernels.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/src/moments.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/moments.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/mdtraj/geometry/drid.o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/dridkernels.o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/moments.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/drid.cpython-312-aarch64-linux-gnu.so building 'mdtraj.geometry.neighbors' extension aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/neighbors.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/neighbors.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/src/neighbors.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/neighbors.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/mdtraj/geometry/neighbors.o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/neighbors.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/neighbors.cpython-312-aarch64-linux-gnu.so building 'mdtraj.geometry.neighborlist' extension aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/neighborlist.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/neighborlist.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/src/neighborlist.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/neighborlist.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/mdtraj/geometry/neighborlist.o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/neighborlist.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/neighborlist.cpython-312-aarch64-linux-gnu.so running install_lib creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/_lprmsd.cpython-312-aarch64-linux-gnu.so -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/_rmsd.cpython-312-aarch64-linux-gnu.so -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/__pycache__/_version.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/__pycache__ creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/__pycache__/trajectory.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/__pycache__/selection.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/__pycache__/residue_names.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/__pycache__/topology.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/__pycache__/element.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/__pycache__ creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/lib copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/lib/center.h -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/lib copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/lib/theobald_rmsd.h -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/lib copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/lib/libtheobald.a -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/lib copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/__init__.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/element.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/residue_names.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/selection.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/topology.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/trajectory.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/dtr.cpython-312-aarch64-linux-gnu.so -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/dcd.cpython-312-aarch64-linux-gnu.so -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/trr.cpython-312-aarch64-linux-gnu.so -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/xtc.cpython-312-aarch64-linux-gnu.so -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/openmmxml.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/psf.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/prmtop.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/mol2.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/hoomdxml.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/gsd.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/xyzfile.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/pdbx.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/netcdf.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/mdcrd.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/lh5.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/lammpstrj.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/hdf5.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/gro.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/arc.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/registry.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/amberrst.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb/__pycache__/pdbstructure.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb/__pycache__/pdbfile.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb/__pycache__ creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb/data copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb/data/pdbNames.xml -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb/data copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb/data/residues.xml -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb/data copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb/__init__.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb/pdbfile.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb/pdbstructure.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__init__.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/amberrst.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/arc.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/gro.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/gsd.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/hdf5.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/hoomdxml.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/lammpstrj.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/lh5.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/mdcrd.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/mol2.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/netcdf.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/openmmxml.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdbx.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/prmtop.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/psf.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/registry.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/xyzfile.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/neighborlist.cpython-312-aarch64-linux-gnu.so -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/neighbors.cpython-312-aarch64-linux-gnu.so -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/drid.cpython-312-aarch64-linux-gnu.so -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/_geometry.cpython-312-aarch64-linux-gnu.so -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/thermodynamic_properties.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/shape.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/sasa.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/rg.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/rdf.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/order.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/hbond.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/dssp.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/dihedral.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/contact.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/distance.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/angle.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__init__.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/alignment.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/angle.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/contact.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/dihedral.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/distance.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/dssp.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/hbond.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/internal.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/order.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/rdf.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/rg.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/sasa.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/shape.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/thermodynamic_properties.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/nmr creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/nmr/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/nmr/__pycache__/shift_wrappers.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/nmr/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/nmr/__pycache__/scalar_couplings.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/nmr/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/nmr/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/nmr/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/nmr/__init__.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/nmr copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/nmr/scalar_couplings.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/nmr copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/nmr/shift_wrappers.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/nmr creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/__pycache__/xtcreporter.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/__pycache__/netcdfreporter.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/__pycache__/hdf5reporter.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/__pycache__/basereporter.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/__pycache__/dcdreporter.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/__init__.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/basereporter.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/dcdreporter.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/hdf5reporter.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/netcdfreporter.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/xtcreporter.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/scripts creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/scripts/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/scripts/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/scripts/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/scripts/__init__.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/scripts copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/scripts/mdconvert.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/scripts copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/scripts/mdinspect.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/scripts creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing/__pycache__/testing.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing/__pycache__/docscrape.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing/__pycache__/docstrings.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing/__init__.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing/docscrape.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing/docstrings.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing/testing.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/__pycache__/singleton.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/__pycache__/zipped.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/__pycache__/unitcell.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/__pycache__/validation.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/__pycache__/rotation.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/__pycache__/delay_import.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/__pycache__/contextmanagers.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/__pycache__ creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/__pycache__/quantity.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/__pycache__/unit_operators.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/__pycache__/basedimension.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/__pycache__/standard_dimensions.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/__pycache__/mymatrix.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/__pycache__/unit.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/__pycache__/prefix.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/__pycache__/baseunit.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/__pycache__/unit_definitions.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/__init__.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/mymatrix.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/constants.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/prefix.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/quantity.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/standard_dimensions.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/unit_definitions.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/unit_math.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/unit_operators.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/basedimension.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/baseunit.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/doctests.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/unit.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/__init__.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/contextmanagers.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/delay_import.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/rotation.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/singleton.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unitcell.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/validation.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/zipped.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/__init__.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/_version.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/io.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/element.py to element.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/residue_names.py to residue_names.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/selection.py to selection.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/topology.py to topology.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/trajectory.py to trajectory.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb/pdbfile.py to pdbfile.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb/pdbstructure.py to pdbstructure.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/amberrst.py to amberrst.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/arc.py to arc.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/gro.py to gro.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/gsd.py to gsd.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/hdf5.py to hdf5.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/hoomdxml.py to hoomdxml.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/lammpstrj.py to lammpstrj.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/lh5.py to lh5.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/mdcrd.py to mdcrd.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/mol2.py to mol2.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/netcdf.py to netcdf.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/openmmxml.py to openmmxml.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdbx.py to pdbx.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/prmtop.py to prmtop.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/psf.py to psf.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/registry.py to registry.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/xyzfile.py to xyzfile.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/alignment.py to alignment.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/angle.py to angle.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/contact.py to contact.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/dihedral.py to dihedral.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/distance.py to distance.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/dssp.py to dssp.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/hbond.py to hbond.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/internal.py to internal.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/order.py to order.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/rdf.py to rdf.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/rg.py to rg.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/sasa.py to sasa.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/shape.py to shape.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/thermodynamic_properties.py to thermodynamic_properties.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/nmr/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/nmr/scalar_couplings.py to scalar_couplings.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/nmr/shift_wrappers.py to shift_wrappers.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/basereporter.py to basereporter.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/dcdreporter.py to dcdreporter.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/hdf5reporter.py to hdf5reporter.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/netcdfreporter.py to netcdfreporter.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/xtcreporter.py to xtcreporter.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/scripts/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/scripts/mdconvert.py to mdconvert.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/scripts/mdinspect.py to mdinspect.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing/docscrape.py to docscrape.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing/docstrings.py to docstrings.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing/testing.py to testing.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/mymatrix.py to mymatrix.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/constants.py to constants.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/prefix.py to prefix.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/quantity.py to quantity.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/standard_dimensions.py to standard_dimensions.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/unit_definitions.py to unit_definitions.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/unit_math.py to unit_math.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/unit_operators.py to unit_operators.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/basedimension.py to basedimension.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/baseunit.py to baseunit.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/doctests.py to doctests.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/unit.py to unit.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/contextmanagers.py to contextmanagers.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/delay_import.py to delay_import.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/rotation.py to rotation.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/singleton.py to singleton.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unitcell.py to unitcell.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/validation.py to validation.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/zipped.py to zipped.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/_version.py to _version.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/io.py to io.cpython-312.pyc running install_egg_info running egg_info creating mdtraj.egg-info writing mdtraj.egg-info/PKG-INFO writing dependency_links to mdtraj.egg-info/dependency_links.txt writing entry points to mdtraj.egg-info/entry_points.txt writing requirements to mdtraj.egg-info/requires.txt writing top-level names to mdtraj.egg-info/top_level.txt writing manifest file 'mdtraj.egg-info/SOURCES.txt' dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative reading manifest file 'mdtraj.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' no previously-included directories found matching '__pycache__' no previously-included directories found matching '*.pyc' adding license file 'LICENSE' writing manifest file 'mdtraj.egg-info/SOURCES.txt' Copying mdtraj.egg-info to /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj-1.10.1.egg-info Skipping SOURCES.txt running install_scripts Installing mdconvert-mdtraj script to /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/bin Installing mdinspect script to /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/bin debian/rules execute_after_dh_auto_install-indep make[1]: Entering directory '/build/reproducible-path/mdtraj-1.10.1' cp -a /build/reproducible-path/mdtraj-1.10.1/examples /build/reproducible-path/mdtraj-1.10.1/examples.orig mkdir -p /build/reproducible-path/mdtraj-1.10.1/build/html/examples/iterload ln -s /build/reproducible-path/mdtraj-1.10.1/examples/data /build/reproducible-path/mdtraj-1.10.1/build/html/examples/iterload/data sed "s|http://www.rcsb.org/pdb/files|/build/reproducible-path/mdtraj-1.10.1/debian/external|g" -i /build/reproducible-path/mdtraj-1.10.1/examples/*.ipynb PYTHONPATH=/build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build \ MPLCONFIGDIR=/build/reproducible-path/mdtraj-1.10.1/build/matplotlib \ make -C docs BUILDDIR=/build/reproducible-path/mdtraj-1.10.1/build html make[2]: Entering directory '/build/reproducible-path/mdtraj-1.10.1/docs' sphinx-build -b html -d /build/reproducible-path/mdtraj-1.10.1/build/doctrees . /build/reproducible-path/mdtraj-1.10.1/build/html Running Sphinx v7.4.7 WARNING: Calling get_html_theme_path is deprecated. If you are calling it to define html_theme_path, you are safe to remove that code. loading translations [en]... done Converting `source_suffix = '.rst'` to `source_suffix = {'.rst': 'restructuredtext'}`. [autosummary] generating autosummary for: analysis.rst, api/reporters.rst, api/trajectory_files.rst, api/utils.rst, atom_selection.rst, building_docs.rst, examples/atom-selection.rst, examples/centroids.rst, examples/clustering.rst, examples/hbonds.rst, ..., notebook-examples/iterload.nblink, notebook-examples/native-contact.nblink, notebook-examples/openmm.nblink, notebook-examples/pca.nblink, notebook-examples/ramachandran-plot.nblink, notebook-examples/rmsd-benchmark.nblink, notebook-examples/rmsd-drift.nblink, notebook-examples/solvent-accessible-surface-area.nblink, notebook-examples/two-pass-clustering.nblink, whatsnew.rst [autosummary] generating autosummary for: /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.Topology.rst, /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.Trajectory.rst, /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.Trajectory.superpose.rst, /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.acylindricity.rst, /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.asphericity.rst, /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.baker_hubbard.rst, /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.chemical_shifts_ppm.rst, /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.chemical_shifts_shiftx2.rst, /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.chemical_shifts_spartaplus.rst, /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.compute_J3_HN_C.rst, ..., /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.utils.check_random_state.rst, /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.utils.ensure_type.rst, /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.utils.ilen.rst, /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.utils.import_.rst, /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.utils.in_units_of.rst, /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.utils.lengths_and_angles_to_box_vectors.rst, /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.utils.rotation_matrix_from_quaternion.rst, /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.utils.timing.rst, /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.utils.uniform_quaternion.rst, /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.wernet_nilsson.rst building [mo]: targets for 0 po files that are out of date writing output... building [html]: targets for 44 source files that are out of date updating environment: [new config] 140 added, 0 changed, 0 removed reading sources... [ 1%] analysis reading sources... [ 1%] api/generated/mdtraj.Topology /usr/lib/python3/dist-packages/numpydoc/docscrape.py:455: UserWarning: potentially wrong underline length... Returns ---------- in Get the indices of biologically-relevant groups by name. ... in the docstring of select_atom_indices in /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_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... [ 4%] 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... [ 6%] 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... [ 9%] api/generated/mdtraj.compute_J3_HN_HA reading sources... [ 10%] api/generated/mdtraj.compute_angles reading sources... [ 11%] api/generated/mdtraj.compute_center_of_mass reading sources... [ 11%] api/generated/mdtraj.compute_chi1 reading sources... [ 12%] api/generated/mdtraj.compute_chi2 reading sources... [ 13%] api/generated/mdtraj.compute_chi3 reading sources... [ 14%] api/generated/mdtraj.compute_chi4 reading sources... [ 14%] api/generated/mdtraj.compute_contacts reading sources... [ 15%] api/generated/mdtraj.compute_dihedrals reading sources... [ 16%] api/generated/mdtraj.compute_directors reading sources... [ 16%] api/generated/mdtraj.compute_displacements reading sources... [ 17%] api/generated/mdtraj.compute_distances reading sources... [ 18%] api/generated/mdtraj.compute_drid reading sources... [ 19%] api/generated/mdtraj.compute_dssp reading sources... [ 19%] api/generated/mdtraj.compute_gyration_tensor reading sources... [ 20%] api/generated/mdtraj.compute_inertia_tensor reading sources... [ 21%] api/generated/mdtraj.compute_neighbors reading sources... [ 21%] api/generated/mdtraj.compute_nematic_order reading sources... [ 22%] api/generated/mdtraj.compute_omega reading sources... [ 23%] api/generated/mdtraj.compute_phi reading sources... [ 24%] api/generated/mdtraj.compute_psi reading sources... [ 24%] api/generated/mdtraj.compute_rdf reading sources... [ 25%] api/generated/mdtraj.compute_rg reading sources... [ 26%] api/generated/mdtraj.density reading sources... [ 26%] api/generated/mdtraj.dipole_moments reading sources... [ 27%] api/generated/mdtraj.formats.AmberNetCDFRestartFile reading sources... [ 28%] api/generated/mdtraj.formats.AmberRestartFile reading sources... [ 29%] api/generated/mdtraj.formats.ArcTrajectoryFile reading sources... [ 29%] api/generated/mdtraj.formats.DCDTrajectoryFile reading sources... [ 30%] api/generated/mdtraj.formats.DTRTrajectoryFile reading sources... [ 31%] api/generated/mdtraj.formats.GroTrajectoryFile reading sources... [ 31%] api/generated/mdtraj.formats.HDF5TrajectoryFile reading sources... [ 32%] api/generated/mdtraj.formats.LAMMPSTrajectoryFile reading sources... [ 33%] api/generated/mdtraj.formats.LH5TrajectoryFile reading sources... [ 34%] api/generated/mdtraj.formats.MDCRDTrajectoryFile reading sources... [ 34%] api/generated/mdtraj.formats.NetCDFTrajectoryFile reading sources... [ 35%] api/generated/mdtraj.formats.PDBTrajectoryFile reading sources... [ 36%] api/generated/mdtraj.formats.TRRTrajectoryFile reading sources... [ 36%] api/generated/mdtraj.formats.XTCTrajectoryFile reading sources... [ 37%] api/generated/mdtraj.formats.XYZTrajectoryFile reading sources... [ 38%] api/generated/mdtraj.geometry.squareform reading sources... [ 39%] api/generated/mdtraj.isothermal_compressability_kappa_T reading sources... [ 39%] api/generated/mdtraj.iterload reading sources... [ 40%] api/generated/mdtraj.join reading sources... [ 41%] api/generated/mdtraj.kabsch_sander reading sources... [ 41%] api/generated/mdtraj.load reading sources... [ 42%] api/generated/mdtraj.load_arc reading sources... [ 43%] api/generated/mdtraj.load_dcd reading sources... [ 44%] api/generated/mdtraj.load_dtr reading sources... [ 44%] api/generated/mdtraj.load_frame reading sources... [ 45%] api/generated/mdtraj.load_hdf5 reading sources... [ 46%] api/generated/mdtraj.load_hoomdxml reading sources... [ 46%] api/generated/mdtraj.load_lammpstrj reading sources... [ 47%] api/generated/mdtraj.load_lh5 reading sources... [ 48%] api/generated/mdtraj.load_netcdf reading sources... [ 49%] api/generated/mdtraj.load_pdb reading sources... [ 49%] api/generated/mdtraj.load_prmtop reading sources... [ 50%] api/generated/mdtraj.load_trr reading sources... [ 51%] api/generated/mdtraj.load_xml reading sources... [ 51%] api/generated/mdtraj.load_xtc reading sources... [ 52%] api/generated/mdtraj.load_xyz reading sources... [ 53%] api/generated/mdtraj.lprmsd reading sources... [ 54%] api/generated/mdtraj.open reading sources... [ 54%] api/generated/mdtraj.principal_moments reading sources... [ 55%] api/generated/mdtraj.reindex_dataframe_by_atoms reading sources... [ 56%] api/generated/mdtraj.relative_shape_antisotropy reading sources... [ 56%] api/generated/mdtraj.reporters.DCDReporter reading sources... [ 57%] api/generated/mdtraj.reporters.HDF5Reporter reading sources... [ 58%] api/generated/mdtraj.reporters.NetCDFReporter reading sources... [ 59%] api/generated/mdtraj.rmsd reading sources... [ 59%] api/generated/mdtraj.rmsf reading sources... [ 60%] api/generated/mdtraj.shrake_rupley reading sources... [ 61%] api/generated/mdtraj.static_dielectric reading sources... [ 61%] api/generated/mdtraj.thermal_expansion_alpha_P reading sources... [ 62%] api/generated/mdtraj.utils.box_vectors_to_lengths_and_angles reading sources... [ 63%] api/generated/mdtraj.utils.check_random_state reading sources... [ 64%] api/generated/mdtraj.utils.ensure_type reading sources... [ 64%] api/generated/mdtraj.utils.ilen reading sources... [ 65%] api/generated/mdtraj.utils.import_ reading sources... [ 66%] api/generated/mdtraj.utils.in_units_of reading sources... [ 66%] api/generated/mdtraj.utils.lengths_and_angles_to_box_vectors reading sources... [ 67%] api/generated/mdtraj.utils.rotation_matrix_from_quaternion reading sources... [ 68%] api/generated/mdtraj.utils.timing reading sources... [ 69%] api/generated/mdtraj.utils.uniform_quaternion reading sources... [ 69%] api/generated/mdtraj.wernet_nilsson reading sources... [ 70%] api/reporters reading sources... [ 71%] api/trajectory_files reading sources... [ 71%] api/utils reading sources... [ 72%] atom_selection reading sources... [ 73%] building_docs reading sources... [ 74%] examples/atom-selection reading sources... [ 74%] examples/centroids reading sources... [ 75%] examples/clustering reading sources... [ 76%] examples/hbonds reading sources... [ 76%] examples/index reading sources... [ 77%] examples/introduction reading sources... [ 78%] examples/iterload reading sources... [ 79%] examples/native-contact reading sources... [ 79%] examples/nmr reading sources... [ 80%] examples/openmm reading sources... [ 81%] examples/pca reading sources... [ 81%] examples/ramachandran-plot reading sources... [ 82%] examples/rmsd-benchmark reading sources... [ 83%] examples/solvent-accessible-surface-area reading sources... [ 84%] examples/two-pass-clustering reading sources... [ 84%] faq reading sources... [ 85%] hdf5_format reading sources... [ 86%] index reading sources... [ 86%] installation reading sources... [ 87%] load_functions reading sources... [ 88%] mdconvert reading sources... [ 89%] new_to_python reading sources... [ 89%] notebook-examples/atom-selection reading sources... [ 90%] notebook-examples/centroids reading sources... [ 91%] notebook-examples/clustering reading sources... [ 91%] notebook-examples/hbonds reading sources... [ 92%] notebook-examples/index reading sources... [ 93%] notebook-examples/introduction reading sources... [ 94%] notebook-examples/iterload reading sources... [ 94%] notebook-examples/native-contact reading sources... [ 95%] notebook-examples/openmm reading sources... [ 96%] notebook-examples/pca reading sources... [ 96%] notebook-examples/ramachandran-plot reading sources... [ 97%] notebook-examples/rmsd-benchmark reading sources... [ 98%] notebook-examples/rmsd-drift reading sources... [ 99%] notebook-examples/solvent-accessible-surface-area reading sources... [ 99%] notebook-examples/two-pass-clustering reading sources... [100%] whatsnew /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/shape.py:docstring of mdtraj.geometry.shape.asphericity:9: WARNING: Block quote ends without a blank line; unexpected unindent. /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/contact.py:docstring of mdtraj.geometry.contact.compute_contacts:9: WARNING: Block quote ends without a blank line; unexpected unindent. /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/contact.py:docstring of mdtraj.geometry.contact.compute_contacts:36: ERROR: Unexpected indentation. /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/contact.py:docstring of mdtraj.geometry.contact.compute_contacts:45: WARNING: Block quote ends without a blank line; unexpected unindent. docstring of mdtraj.formats.dtr.load_dtr:7: ERROR: Unexpected indentation. /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/shape.py:docstring of mdtraj.geometry.shape.relative_shape_anisotropy:9: WARNING: Block quote ends without a blank line; unexpected unindent. /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/shape.py:docstring of mdtraj.geometry.shape.relative_shape_anisotropy:11: ERROR: Unexpected indentation. /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/shape.py:docstring of mdtraj.geometry.shape.relative_shape_anisotropy:12: WARNING: Block quote ends without a blank line; unexpected unindent. /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/shape.py:docstring of mdtraj.geometry.shape.relative_shape_anisotropy:14: WARNING: Definition list ends without a blank line; unexpected unindent. /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/shape.py:docstring of mdtraj.geometry.shape.relative_shape_anisotropy:15: WARNING: Block quote ends without a blank line; unexpected unindent. /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/rotation.py:docstring of mdtraj.utils.rotation.uniform_quaternion:37: 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/reproducible-path/mdtraj-1.10.1/docs/examples/atom-selection.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/atom-selection.ipynb :skip_exceptions: /build/reproducible-path/mdtraj-1.10.1/docs/examples/centroids.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/centroids.ipynb :skip_exceptions: /build/reproducible-path/mdtraj-1.10.1/docs/examples/clustering.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/clustering.ipynb :skip_exceptions: /build/reproducible-path/mdtraj-1.10.1/docs/examples/hbonds.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/hbonds.ipynb :skip_exceptions: /build/reproducible-path/mdtraj-1.10.1/docs/examples/iterload.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/iterload.ipynb :skip_exceptions: /build/reproducible-path/mdtraj-1.10.1/docs/examples/native-contact.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/native-contact.ipynb :skip_exceptions: /build/reproducible-path/mdtraj-1.10.1/docs/examples/nmr.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/nmr.ipynb :skip_exceptions: /build/reproducible-path/mdtraj-1.10.1/docs/examples/openmm.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/simulation-with-openmm.ipynb :skip_exceptions: /build/reproducible-path/mdtraj-1.10.1/docs/examples/pca.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/principal-components.ipynb :skip_exceptions: /build/reproducible-path/mdtraj-1.10.1/docs/examples/ramachandran-plot.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/ramachandran-plot.ipynb :skip_exceptions: /build/reproducible-path/mdtraj-1.10.1/docs/examples/rmsd-benchmark.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/rmsd-benchmark.ipynb :skip_exceptions: /build/reproducible-path/mdtraj-1.10.1/docs/examples/solvent-accessible-surface-area.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/solvent-accessible-surface-area.ipynb :skip_exceptions: /build/reproducible-path/mdtraj-1.10.1/docs/examples/two-pass-clustering.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/two-pass-clustering.ipynb :skip_exceptions: /build/reproducible-path/mdtraj-1.10.1/docs/index.rst:26: WARNING: toctree contains reference to nonexisting document '.. examples/index' /build/reproducible-path/mdtraj-1.10.1/docs/installation.rst:1: WARNING: malformed hyperlink target. /build/reproducible-path/mdtraj-1.10.1/docs/mdconvert.rst:2: WARNING: Title underline too short. ``mdconvert`` (``mdconvert-mdtraj``) ============= /build/reproducible-path/mdtraj-1.10.1/docs/whatsnew.rst:60: WARNING: Title underline too short. v1.9.9 (July 22, 2023) --------------------- /build/reproducible-path/mdtraj-1.10.1/docs/whatsnew.rst:60: WARNING: Title underline too short. v1.9.9 (July 22, 2023) --------------------- /build/reproducible-path/mdtraj-1.10.1/docs/whatsnew.rst:115: WARNING: Title underline too short. v1.9.7 (November 12, 2021) ----------------------- /build/reproducible-path/mdtraj-1.10.1/docs/whatsnew.rst:115: WARNING: Title underline too short. v1.9.7 (November 12, 2021) ----------------------- looking for now-outdated files... none found pickling environment... WARNING: cannot cache unpickable configuration value: 'nbsphinx_custom_formats' (because it contains a function, class, or module object) done checking consistency... /build/reproducible-path/mdtraj-1.10.1/docs/building_docs.rst: WARNING: document isn't included in any toctree /build/reproducible-path/mdtraj-1.10.1/docs/examples/index.rst: WARNING: document isn't included in any toctree /build/reproducible-path/mdtraj-1.10.1/docs/faq.rst: WARNING: document isn't included in any toctree /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.chemical_shifts_ppm.rst:24: WARNING: Citation [R580094b12b10-1] is not referenced. /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.chemical_shifts_shiftx2.rst:27: WARNING: Citation [R32f229ae9dd9-1] is not referenced. /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.chemical_shifts_spartaplus.rst:30: WARNING: Citation [R85224fbb9dbc-1] is not referenced. /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.compute_J3_HN_C.rst:24: WARNING: Citation [R44e9b977b917-1] is not referenced. /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.compute_J3_HN_CB.rst:24: WARNING: Citation [Red2371ebcd94-1] is not referenced. /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.compute_J3_HN_HA.rst:25: WARNING: Citation [Rcea8e821fb69-1] is not referenced. /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.compute_J3_HN_HA.rst:30: WARNING: Citation [Rcea8e821fb69-2] is not referenced. /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.compute_J3_HN_HA.rst:35: WARNING: Citation [Rcea8e821fb69-3] is not referenced. /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.compute_directors.rst:33: WARNING: Citation [R476bbf639532-1] is not referenced. /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.compute_drid.rst:19: WARNING: Citation [Rb9f983981da1-1] is not referenced. /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.compute_dssp.rst:43: WARNING: Citation [Rb487c1f2550c-1] is not referenced. /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.compute_gyration_tensor.rst:18: WARNING: Citation [Rc72b27c79197-1] is not referenced. /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.compute_nematic_order.rst:25: WARNING: Citation [R38e8a5b92b1b-1] is not referenced. /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.compute_nematic_order.rst:27: WARNING: Citation [R38e8a5b92b1b-2] is not referenced. /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.compute_nematic_order.rst:28: WARNING: Citation [R38e8a5b92b1b-3] is not referenced. /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.kabsch_sander.rst:33: WARNING: Citation [Rd51ca7d055fd-1] is not referenced. /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.shrake_rupley.rst:68: WARNING: Citation [Re2ba905e251a-1] is not referenced. /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.utils.rotation_matrix_from_quaternion.rst:20: WARNING: Citation [R7dd18c0d2619-1] is not referenced. done preparing documents... done copying assets... copying static files... done copying extra files... done copying assets: done writing output... [ 1%] 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... [ 4%] 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... [ 6%] 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... [ 9%] api/generated/mdtraj.compute_J3_HN_HA writing output... [ 10%] api/generated/mdtraj.compute_angles writing output... [ 11%] api/generated/mdtraj.compute_center_of_mass writing output... [ 11%] api/generated/mdtraj.compute_chi1 writing output... [ 12%] api/generated/mdtraj.compute_chi2 writing output... [ 13%] api/generated/mdtraj.compute_chi3 writing output... [ 14%] api/generated/mdtraj.compute_chi4 writing output... [ 14%] api/generated/mdtraj.compute_contacts writing output... [ 15%] api/generated/mdtraj.compute_dihedrals writing output... [ 16%] api/generated/mdtraj.compute_directors writing output... [ 16%] api/generated/mdtraj.compute_displacements writing output... [ 17%] api/generated/mdtraj.compute_distances writing output... [ 18%] api/generated/mdtraj.compute_drid writing output... [ 19%] api/generated/mdtraj.compute_dssp writing output... [ 19%] api/generated/mdtraj.compute_gyration_tensor writing output... [ 20%] api/generated/mdtraj.compute_inertia_tensor writing output... [ 21%] api/generated/mdtraj.compute_neighbors writing output... [ 21%] api/generated/mdtraj.compute_nematic_order writing output... [ 22%] api/generated/mdtraj.compute_omega writing output... [ 23%] api/generated/mdtraj.compute_phi writing output... [ 24%] api/generated/mdtraj.compute_psi writing output... [ 24%] api/generated/mdtraj.compute_rdf writing output... [ 25%] api/generated/mdtraj.compute_rg writing output... [ 26%] api/generated/mdtraj.density writing output... [ 26%] api/generated/mdtraj.dipole_moments writing output... [ 27%] api/generated/mdtraj.formats.AmberNetCDFRestartFile writing output... [ 28%] api/generated/mdtraj.formats.AmberRestartFile writing output... [ 29%] api/generated/mdtraj.formats.ArcTrajectoryFile writing output... [ 29%] api/generated/mdtraj.formats.DCDTrajectoryFile writing output... [ 30%] api/generated/mdtraj.formats.DTRTrajectoryFile writing output... [ 31%] api/generated/mdtraj.formats.GroTrajectoryFile writing output... [ 31%] api/generated/mdtraj.formats.HDF5TrajectoryFile writing output... [ 32%] api/generated/mdtraj.formats.LAMMPSTrajectoryFile writing output... 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[ 81%] examples/pca writing output... [ 81%] examples/ramachandran-plot writing output... [ 82%] examples/rmsd-benchmark writing output... [ 83%] examples/solvent-accessible-surface-area writing output... [ 84%] examples/two-pass-clustering writing output... [ 84%] faq writing output... [ 85%] hdf5_format writing output... [ 86%] index writing output... [ 86%] installation writing output... [ 87%] load_functions writing output... [ 88%] mdconvert writing output... [ 89%] new_to_python writing output... [ 89%] notebook-examples/atom-selection writing output... [ 90%] notebook-examples/centroids writing output... [ 91%] notebook-examples/clustering writing output... [ 91%] notebook-examples/hbonds writing output... [ 92%] notebook-examples/index writing output... [ 93%] notebook-examples/introduction writing output... [ 94%] notebook-examples/iterload writing output... [ 94%] notebook-examples/native-contact writing output... [ 95%] notebook-examples/openmm writing output... [ 96%] notebook-examples/pca writing output... [ 96%] notebook-examples/ramachandran-plot writing output... [ 97%] notebook-examples/rmsd-benchmark writing output... [ 98%] notebook-examples/rmsd-drift writing output... [ 99%] notebook-examples/solvent-accessible-surface-area writing output... [ 99%] notebook-examples/two-pass-clustering writing output... [100%] whatsnew generating indices... genindex done copying linked files... copying notebooks ... [ 8%] notebook-examples/atom-selection.ipynb copying notebooks ... [ 15%] notebook-examples/centroids.ipynb copying notebooks ... [ 23%] notebook-examples/clustering.ipynb copying notebooks ... [ 31%] notebook-examples/hbonds.ipynb copying notebooks ... [ 38%] notebook-examples/iterload.ipynb copying notebooks ... [ 46%] notebook-examples/native-contact.ipynb copying notebooks ... [ 54%] notebook-examples/openmm.ipynb copying notebooks ... [ 62%] notebook-examples/pca.ipynb copying notebooks ... 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[ 96%] mdtraj.utils.unit highlighting module code... [ 98%] mdtraj.utils.unitcell highlighting module code... [100%] mdtraj.utils.validation writing additional pages... search done copying images... [ 11%] ../build/doctrees/nbsphinx/notebook-examples_clustering_11_0.png copying images... [ 22%] ../build/doctrees/nbsphinx/notebook-examples_hbonds_9_1.png copying images... [ 33%] ../build/doctrees/nbsphinx/notebook-examples_native-contact_6_0.png copying images... [ 44%] ../build/doctrees/nbsphinx/notebook-examples_pca_9_0.png copying images... [ 56%] ../build/doctrees/nbsphinx/notebook-examples_pca_12_0.png copying images... [ 67%] ../build/doctrees/nbsphinx/notebook-examples_ramachandran-plot_7_1.png copying images... [ 78%] ../build/doctrees/nbsphinx/notebook-examples_rmsd-drift_7_1.png copying images... [ 89%] ../build/doctrees/nbsphinx/notebook-examples_solvent-accessible-surface-area_8_0.png copying images... [100%] ../build/doctrees/nbsphinx/notebook-examples_solvent-accessible-surface-area_10_0.png dumping search index in English (code: en)... done dumping object inventory... done build succeeded, 54 warnings. The HTML pages are in ../build/html. Build finished. The HTML pages are in /build/reproducible-path/mdtraj-1.10.1/build/html. make[2]: Leaving directory '/build/reproducible-path/mdtraj-1.10.1/docs' for img in `find /build/reproducible-path/mdtraj-1.10.1/build/html/examples -name *.png`; do \ mv $img /build/reproducible-path/mdtraj-1.10.1/build/html/examples; \ done sed "s|/build/reproducible-path/mdtraj-1.10.1/build/html/examples/|./|g; s|.ipynb|.ipynb.gz|g" -i /build/reproducible-path/mdtraj-1.10.1/build/html/examples/*.html sed "s|/build/reproducible-path/mdtraj-1.10.1/debian/external|http://www.rcsb.org/pdb/files|g" -i /build/reproducible-path/mdtraj-1.10.1/build/html/examples/*.html rm /build/reproducible-path/mdtraj-1.10.1/build/html/examples/iterload/data rm -rf /build/reproducible-path/mdtraj-1.10.1/examples mv /build/reproducible-path/mdtraj-1.10.1/examples.orig /build/reproducible-path/mdtraj-1.10.1/examples make[1]: Leaving directory '/build/reproducible-path/mdtraj-1.10.1' dh_install -O--buildsystem=pybuild install -m0755 -d debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples/data cp --reflink=auto -a ./debian/external/2EQQ.pdb ./debian/external/2MI7.pdb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples/data/ install -m0755 -d debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/doi-10.1016_j.bpj.2015.08.015-blue.svg cp --reflink=auto -a ./debian/external/doi-10.1016_j.bpj.2015.08.015-blue.svg debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/doi-10.1016_j.bpj.2015.08.015-blue.svg/ dh_installdocs -O--buildsystem=pybuild dh_installdocs: warning: Cannot auto-detect main package for python-mdtraj-doc. If the default is wrong, please use --doc-main-package install -m0755 -d debian/python3-mdtraj/usr/share/doc/python3-mdtraj install -p -m0644 debian/copyright debian/python3-mdtraj/usr/share/doc/python3-mdtraj/copyright install -m0755 -d debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc cd './build/html/..' && find 'html' \( -type f -or -type l \) -and ! -empty -print0 | LC_ALL=C sort -z | xargs -0 -I {} cp --reflink=auto --parents -dp {} /build/reproducible-path/mdtraj-1.10.1/debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc cp --reflink=auto -a ./README.md debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc chmod -R u\+rw,go=rX debian/python-mdtraj-doc/usr/share/doc install -p -m0644 debian/copyright debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/copyright install -m0755 -d debian/python-mdtraj-doc/usr/share/doc-base/ install -p -m0644 debian/python-mdtraj-doc.doc-base debian/python-mdtraj-doc/usr/share/doc-base/python-mdtraj-doc.mdtraj debian/rules override_dh_sphinxdoc-indep make[1]: Entering directory '/build/reproducible-path/mdtraj-1.10.1' dh_sphinxdoc -i ln -sf ../../../../../sphinx_rtd_theme/static/js/theme.js debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/js/theme.js ln -sf ../../../../../sphinx_rtd_theme/static/fonts/fontawesome-webfont.woff2 debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.woff2 ln -sf ../../../../../sphinx_rtd_theme/static/fonts/fontawesome-webfont.woff debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.woff ln -sf ../../../../../sphinx_rtd_theme/static/fonts/fontawesome-webfont.ttf debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.ttf ln -sf ../../../../../sphinx_rtd_theme/static/fonts/fontawesome-webfont.svg debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.svg ln -sf 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../../../../../sphinx_rtd_theme/static/css/badge_only.css debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/css/badge_only.css ln -sf ../../../../javascript/sphinxdoc/1.0/language_data.js debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/language_data.js ln -sf ../../../../javascript/sphinxdoc/1.0/searchtools.js debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/searchtools.js ln -sf ../../../../javascript/sphinxdoc/1.0/doctools.js debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/doctools.js ln -sf ../../../../javascript/sphinxdoc/1.0/sphinx_highlight.js debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/sphinx_highlight.js rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/.buildinfo mv debian/python-mdtraj-doc.substvars.new debian/python-mdtraj-doc.substvars mv debian/python-mdtraj-doc.substvars.new debian/python-mdtraj-doc.substvars mv debian/python-mdtraj-doc.substvars.new debian/python-mdtraj-doc.substvars mv debian/python-mdtraj-doc.substvars.new debian/python-mdtraj-doc.substvars mv debian/python-mdtraj-doc.substvars.new debian/python-mdtraj-doc.substvars mv debian/python-mdtraj-doc.substvars.new debian/python-mdtraj-doc.substvars sed "s|src=\"https://img.shields.io/badge/DOI-10.1016%2Fj.bpj.2015.08.015-blue.svg\"|src=\"_static/doi-10.1016_j.bpj.2015.08.015-blue.svg\"|g" -i debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/index.html make[1]: Leaving directory '/build/reproducible-path/mdtraj-1.10.1' dh_sphinxdoc -O--buildsystem=pybuild -Npython-mdtraj-doc dh_sphinxdoc: warning: Sphinx documentation not found dh_installchangelogs -O--buildsystem=pybuild install -m0755 -d debian/python3-mdtraj/usr/share/doc/python3-mdtraj install -p -m0644 debian/.debhelper/generated/python3-mdtraj/dh_installchangelogs.dch.trimmed debian/python3-mdtraj/usr/share/doc/python3-mdtraj/changelog.Debian install -m0755 -d debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc install -p -m0644 debian/.debhelper/generated/python-mdtraj-doc/dh_installchangelogs.dch.trimmed debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/changelog.Debian dh_installexamples -O--buildsystem=pybuild dh_installexamples: warning: Cannot auto-detect main package for python-mdtraj-doc. If the default is wrong, please use --doc-main-package install -m0755 -d debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples cp --reflink=auto -a ./examples/1vii_3frames.pdb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples cp --reflink=auto -a ./examples/ala2.h5 debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples cp --reflink=auto -a ./examples/atom-selection.ipynb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples cp --reflink=auto -a ./examples/centroids.ipynb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples cp --reflink=auto -a ./examples/clustering.ipynb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples cp --reflink=auto -a ./examples/data debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples cp --reflink=auto -a ./examples/hbonds.ipynb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples cp --reflink=auto -a ./examples/iterload.ipynb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples cp --reflink=auto -a ./examples/native-contact.ipynb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples cp --reflink=auto -a ./examples/nmr.ipynb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples cp --reflink=auto -a ./examples/principal-components.ipynb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples cp --reflink=auto -a ./examples/ramachandran-plot.ipynb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples cp --reflink=auto -a ./examples/rmsd-benchmark.ipynb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples cp --reflink=auto -a ./examples/rmsd-drift.ipynb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples cp --reflink=auto -a ./examples/simulation-with-openmm.ipynb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples cp --reflink=auto -a ./examples/solvent-accessible-surface-area.ipynb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples cp --reflink=auto -a ./examples/test_examples.py debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples cp --reflink=auto -a ./examples/two-pass-clustering.ipynb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples dh_installman -O--buildsystem=pybuild install -m0755 -d debian/python3-mdtraj/usr/share/man/man1/ install -p -m0644 ./debian/mdconvert-mdtraj.1 debian/python3-mdtraj/usr/share/man/man1/mdconvert-mdtraj.1 install -m0755 -d debian/python3-mdtraj/usr/share/man/man1/ install -p -m0644 ./debian/mdinspect.1 debian/python3-mdtraj/usr/share/man/man1/mdinspect.1 man-recode --to-code UTF-8 --suffix .dh-new debian/python3-mdtraj/usr/share/man/man1/mdinspect.1 man-recode --to-code UTF-8 --suffix .dh-new debian/python3-mdtraj/usr/share/man/man1/mdconvert-mdtraj.1 mv debian/python3-mdtraj/usr/share/man/man1/mdinspect.1.dh-new debian/python3-mdtraj/usr/share/man/man1/mdinspect.1 chmod 0644 -- debian/python3-mdtraj/usr/share/man/man1/mdinspect.1 mv debian/python3-mdtraj/usr/share/man/man1/mdconvert-mdtraj.1.dh-new debian/python3-mdtraj/usr/share/man/man1/mdconvert-mdtraj.1 chmod 0644 -- debian/python3-mdtraj/usr/share/man/man1/mdconvert-mdtraj.1 dh_python3 -O--buildsystem=pybuild D: dh_python3 dh_python3:180: version: 6.20241024 D: dh_python3 dh_python3:181: argv: ['/usr/bin/dh_python3', '-O--buildsystem=pybuild'] D: dh_python3 dh_python3:182: options: Namespace(guess_deps=True, skip_private=False, verbose=True, arch=None, package=None, no_package=None, remaining_packages=False, compile_all=False, vrange=None, regexpr=None, accept_upstream_versions=False, depends=None, depends_section=None, recommends=None, recommends_section=None, suggests=None, suggests_section=None, requires=None, shebang=None, ignore_shebangs=False, clean_dbg_pkg=True, no_ext_rename=False, no_shebang_rewrite=False, private_dir=None, O=['--buildsystem=pybuild']) D: dh_python3 dh_python3:183: supported Python versions: 3.12 (default=3.12) D: dh_python3 debhelper:166: skipping package python-mdtraj-doc (missing ${python3:Depends} in Depends/Recommends) D: dh_python3 debhelper:174: source=mdtraj, binary packages=['python3-mdtraj'] D: dh_python3 dh_python3:205: processing package python3-mdtraj... D: dh_python3 fs:50: moving files from debian/python3-mdtraj/usr/lib/python3.12/dist-packages to debian/python3-mdtraj/usr/lib/python3/dist-packages/ D: dh_python3 fs:338: package python3-mdtraj details = {'requires.txt': {'debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj-1.10.1.egg-info/requires.txt'}, 'egg-info': {'debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj-1.10.1.egg-info/PKG-INFO'}, 'dist-info': set(), 'nsp.txt': set(), 'shebangs': {/usr/bin/python3, /usr/bin/python3}, 'public_vers': {Version('3')}, 'private_dirs': {}, 'compile': True, 'ext_vers': {Version('3.12')}, 'ext_no_version': set()} D: dh_python3 depends:103: generating dependencies for package python3-mdtraj D: dh_python3 pydist:175: trying to find dependency for numpy<2.0.0a0,>=1.23 (python=None) D: dh_python3 pydist:209: dependency: module seems to be installed D: dh_python3 pydist:284: dependency: included in build-deps D: dh_python3 pydist:175: trying to find dependency for packaging (python=None) D: dh_python3 pydist:209: dependency: module seems to be installed D: dh_python3 pydist:284: dependency: included in build-deps D: dh_python3 pydist:175: trying to find dependency for pyparsing (python=None) D: dh_python3 pydist:209: dependency: module seems to be installed D: dh_python3 pydist:284: dependency: included in build-deps D: dh_python3 pydist:175: trying to find dependency for scipy (python=None) D: dh_python3 pydist:209: dependency: module seems to be installed D: dh_python3 pydist:284: dependency: included in build-deps D: dh_python3 depends:253: D={'python3-scipy', 'python3-numpy', 'python3-pyparsing', 'python3 (<< 3.13)', 'python3:any', 'python3-packaging', 'python3 (>= 3.12~)'}; R=[]; S=[]; E=[], B=[]; RT=[] rm -f debian/python-mdtraj-doc.debhelper.log debian/rules execute_after_dh_python3 make[1]: Entering directory '/build/reproducible-path/mdtraj-1.10.1' dh_numpy3 mv debian/python3-mdtraj.substvars.new debian/python3-mdtraj.substvars mv debian/python-mdtraj-doc.substvars.new debian/python-mdtraj-doc.substvars # setup.py builds the static lib libtheobald.a for each python version # but dh_python3 can't tell the difference between the different builds, # since py3.11 compiles libtheobald.o with -fwrapv, where py3.12 uses -fno-strict-overflow # So clean up manually (assume the binary difference is not an issue) rm -f debian/python3-mdtraj/usr/lib/python3.*/dist-packages/mdtraj/core/lib/libtheobald.a for d in debian/python3-mdtraj/usr/lib/python3.*/dist-packages/mdtraj/core/lib; do if [-d $d]; then rmdir -p --ignore-fail-on-non-empty $d; fi; done /bin/sh: line 1: [-d: command not found make[1]: Leaving directory '/build/reproducible-path/mdtraj-1.10.1' dh_installsystemduser -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/css/theme.css ln -s ../../../../../sphinx_rtd_theme/static/css/theme.css debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/css/theme.css rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/css/badge_only.css ln -s ../../../../../sphinx_rtd_theme/static/css/badge_only.css debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/css/badge_only.css rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.woff2 ln -s ../../../../../sphinx_rtd_theme/static/fonts/fontawesome-webfont.woff2 debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.woff2 rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.woff ln -s ../../../../../sphinx_rtd_theme/static/fonts/fontawesome-webfont.woff debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.woff rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.ttf ln -s ../../../../../sphinx_rtd_theme/static/fonts/fontawesome-webfont.ttf debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.ttf rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.svg ln -s ../../../../../sphinx_rtd_theme/static/fonts/fontawesome-webfont.svg debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.svg rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.eot ln -s ../../../../../sphinx_rtd_theme/static/fonts/fontawesome-webfont.eot debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.eot rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Regular.ttf ln -s ../../../../../sphinx_rtd_theme/static/fonts/Lato-Regular.ttf debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Regular.ttf rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Italic.ttf ln -s ../../../../../sphinx_rtd_theme/static/fonts/Lato-Italic.ttf debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Italic.ttf rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-BoldItalic.ttf ln -s ../../../../../sphinx_rtd_theme/static/fonts/Lato-BoldItalic.ttf debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-BoldItalic.ttf rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Bold.ttf ln -s ../../../../../sphinx_rtd_theme/static/fonts/Lato-Bold.ttf debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Bold.ttf rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/RobotoSlab-Regular.woff2 ln -s ../../../../../sphinx_rtd_theme/static/fonts/RobotoSlab-Regular.woff2 debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/RobotoSlab-Regular.woff2 rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/RobotoSlab-Bold.woff2 ln -s ../../../../../sphinx_rtd_theme/static/fonts/RobotoSlab-Bold.woff2 debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/RobotoSlab-Bold.woff2 rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Regular.woff2 ln -s ../../../../../sphinx_rtd_theme/static/fonts/Lato-Regular.woff2 debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Regular.woff2 rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Italic.woff2 ln -s ../../../../../sphinx_rtd_theme/static/fonts/Lato-Italic.woff2 debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Italic.woff2 rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-BoldItalic.woff2 ln -s ../../../../../sphinx_rtd_theme/static/fonts/Lato-BoldItalic.woff2 debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-BoldItalic.woff2 rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Bold.woff2 ln -s ../../../../../sphinx_rtd_theme/static/fonts/Lato-Bold.woff2 debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Bold.woff2 rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/js/theme.js ln -s ../../../../../sphinx_rtd_theme/static/js/theme.js debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/js/theme.js rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/language_data.js ln -s ../../../../javascript/sphinxdoc/1.0/language_data.js debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/language_data.js rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/searchtools.js ln -s ../../../../javascript/sphinxdoc/1.0/searchtools.js debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/searchtools.js rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/doctools.js ln -s ../../../../javascript/sphinxdoc/1.0/doctools.js debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/doctools.js rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/sphinx_highlight.js ln -s ../../../../javascript/sphinxdoc/1.0/sphinx_highlight.js debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/sphinx_highlight.js dh_strip_nondeterminism -O--buildsystem=pybuild Using 1731351154 as canonical time Normalizing debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_images/notebook-examples_rmsd-drift_7_1.png using File::StripNondeterminism::handlers::png Normalizing debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_images/notebook-examples_ramachandran-plot_7_1.png using File::StripNondeterminism::handlers::png Normalizing debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_images/notebook-examples_solvent-accessible-surface-area_8_0.png using File::StripNondeterminism::handlers::png Normalizing debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_images/notebook-examples_solvent-accessible-surface-area_10_0.png using File::StripNondeterminism::handlers::png Normalizing debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_images/notebook-examples_pca_9_0.png using File::StripNondeterminism::handlers::png Normalizing debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_images/notebook-examples_pca_12_0.png using File::StripNondeterminism::handlers::png Normalizing debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/minus.png using File::StripNondeterminism::handlers::png Normalizing debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/mdtraj_logo-small.png using File::StripNondeterminism::handlers::png Normalizing debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/file.png using File::StripNondeterminism::handlers::png Normalizing debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_images/notebook-examples_clustering_11_0.png using File::StripNondeterminism::handlers::png Normalizing debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/plus.png using File::StripNondeterminism::handlers::png Normalizing debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_images/notebook-examples_native-contact_6_0.png using File::StripNondeterminism::handlers::png Normalizing debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_images/notebook-examples_hbonds_9_1.png using File::StripNondeterminism::handlers::png dh_compress -O--buildsystem=pybuild cd debian/python-mdtraj-doc cd debian/python3-mdtraj chmod a-x usr/share/doc/python-mdtraj-doc/changelog.Debian usr/share/doc/python-mdtraj-doc/html/_static/example-trajectoryview-data.json usr/share/doc/python-mdtraj-doc/html/_static/mdtraj_logo.xcf usr/share/doc/python-mdtraj-doc/html/notebook-examples/atom-selection.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/clustering.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/hbonds.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/iterload.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/native-contact.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/openmm.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/pca.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/ramachandran-plot.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/rmsd-benchmark.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/rmsd-drift.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/solvent-accessible-surface-area.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/two-pass-clustering.ipynb chmod a-x usr/share/doc/python3-mdtraj/changelog.Debian usr/share/man/man1/mdconvert-mdtraj.1 usr/share/man/man1/mdinspect.1 gzip -9nf usr/share/doc/python-mdtraj-doc/changelog.Debian usr/share/doc/python-mdtraj-doc/html/_static/example-trajectoryview-data.json usr/share/doc/python-mdtraj-doc/html/_static/mdtraj_logo.xcf usr/share/doc/python-mdtraj-doc/html/notebook-examples/atom-selection.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/clustering.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/hbonds.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/iterload.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/native-contact.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/openmm.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/pca.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/ramachandran-plot.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/rmsd-benchmark.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/rmsd-drift.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/solvent-accessible-surface-area.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/two-pass-clustering.ipynb gzip -9nf usr/share/doc/python3-mdtraj/changelog.Debian usr/share/man/man1/mdconvert-mdtraj.1 usr/share/man/man1/mdinspect.1 cd '/build/reproducible-path/mdtraj-1.10.1' cd '/build/reproducible-path/mdtraj-1.10.1' dh_fixperms -O--buildsystem=pybuild find debian/python3-mdtraj ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/python-mdtraj-doc ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/python-mdtraj-doc/usr/share/doc -type f -a -true -a ! -regex 'debian/python-mdtraj-doc/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/python3-mdtraj/usr/share/doc -type f -a -true -a ! -regex 'debian/python3-mdtraj/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/python3-mdtraj/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/python-mdtraj-doc/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/python3-mdtraj/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/python-mdtraj-doc -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/python3-mdtraj -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/python3-mdtraj/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x find debian/python3-mdtraj/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w dh_missing -O--buildsystem=pybuild dh_dwz -a -O--buildsystem=pybuild install -m0755 -d debian/python3-mdtraj/usr/lib/debug/.dwz/aarch64-linux-gnu dwz -mdebian/python3-mdtraj/usr/lib/debug/.dwz/aarch64-linux-gnu/python3-mdtraj.debug -M/usr/lib/debug/.dwz/aarch64-linux-gnu/python3-mdtraj.debug -- debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_lprmsd.cpython-312-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_rmsd.cpython-312-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dcd.cpython-312-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dtr.cpython-312-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/trr.cpython-312-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/xtc.cpython-312-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/_geometry.cpython-312-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/drid.cpython-312-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighborlist.cpython-312-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighbors.cpython-312-aarch64-linux-gnu.so objcopy --compress-debug-sections debian/python3-mdtraj/usr/lib/debug/.dwz/aarch64-linux-gnu/python3-mdtraj.debug chmod 0644 -- debian/python3-mdtraj/usr/lib/debug/.dwz/aarch64-linux-gnu/python3-mdtraj.debug dh_strip -a -O--buildsystem=pybuild install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/bc objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_rmsd.cpython-312-aarch64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/bc/92b1cc48da5dbc004c484380dedfb156445836.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/bc/92b1cc48da5dbc004c484380dedfb156445836.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_rmsd.cpython-312-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/bc/92b1cc48da5dbc004c484380dedfb156445836.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_rmsd.cpython-312-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/4c objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_lprmsd.cpython-312-aarch64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/4c/f942d03f0949bc7ba0822d5550cb9f95142f26.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/4c/f942d03f0949bc7ba0822d5550cb9f95142f26.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_lprmsd.cpython-312-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/4c/f942d03f0949bc7ba0822d5550cb9f95142f26.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_lprmsd.cpython-312-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/d4 objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dtr.cpython-312-aarch64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/d4/b2a93673b2221f56780e72a7e1718f0c618c5e.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/d4/b2a93673b2221f56780e72a7e1718f0c618c5e.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dtr.cpython-312-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/d4/b2a93673b2221f56780e72a7e1718f0c618c5e.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dtr.cpython-312-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/6b objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/trr.cpython-312-aarch64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/6b/b159a39c2ff605460df9153d452d2ef8ab4ac6.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/6b/b159a39c2ff605460df9153d452d2ef8ab4ac6.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/trr.cpython-312-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/6b/b159a39c2ff605460df9153d452d2ef8ab4ac6.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/trr.cpython-312-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/61 objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/xtc.cpython-312-aarch64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/61/77875a14b14a42a00f3ca1801eeb87afaed36a.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/61/77875a14b14a42a00f3ca1801eeb87afaed36a.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/xtc.cpython-312-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/61/77875a14b14a42a00f3ca1801eeb87afaed36a.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/xtc.cpython-312-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/6b objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dcd.cpython-312-aarch64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/6b/1f706f0f71d07f901a5add8ffb2c140d4a6ad0.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/6b/1f706f0f71d07f901a5add8ffb2c140d4a6ad0.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dcd.cpython-312-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/6b/1f706f0f71d07f901a5add8ffb2c140d4a6ad0.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dcd.cpython-312-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/92 objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighbors.cpython-312-aarch64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/92/9d0ccd694afdabe67f7feb4a26bd7034a33eab.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/92/9d0ccd694afdabe67f7feb4a26bd7034a33eab.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighbors.cpython-312-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/92/9d0ccd694afdabe67f7feb4a26bd7034a33eab.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighbors.cpython-312-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/35 objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/drid.cpython-312-aarch64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/35/240a209fe480e2b9f0415c22146a7e3347bc0d.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/35/240a209fe480e2b9f0415c22146a7e3347bc0d.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/drid.cpython-312-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/35/240a209fe480e2b9f0415c22146a7e3347bc0d.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/drid.cpython-312-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/f7 objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighborlist.cpython-312-aarch64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/f7/4789370291e76e7ca43144b1499e54431b1d15.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/f7/4789370291e76e7ca43144b1499e54431b1d15.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighborlist.cpython-312-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/f7/4789370291e76e7ca43144b1499e54431b1d15.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighborlist.cpython-312-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/13 objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/_geometry.cpython-312-aarch64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/13/e77ab200d4af0076b47c5faddc43b94a9adb65.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/13/e77ab200d4af0076b47c5faddc43b94a9adb65.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/_geometry.cpython-312-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/13/e77ab200d4af0076b47c5faddc43b94a9adb65.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/_geometry.cpython-312-aarch64-linux-gnu.so strip --strip-debug --remove-section=.comment --remove-section=.note --enable-deterministic-archives -R .gnu.lto_\* -R .gnu.debuglto_\* -N __gnu_lto_slim -N __gnu_lto_v1 debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/core/lib/libtheobald.a install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.dwz cp --reflink=auto -a debian/python3-mdtraj/usr/lib/debug/.dwz/aarch64-linux-gnu debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.dwz rm -fr debian/python3-mdtraj/usr/lib/debug/.dwz rmdir -p --ignore-fail-on-non-empty debian/python3-mdtraj/usr/lib/debug install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/share/doc ln -s python3-mdtraj debian/.debhelper/python3-mdtraj/dbgsym-root/usr/share/doc/python3-mdtraj-dbgsym install -m0755 -d debian/.debhelper/python3-mdtraj dh_makeshlibs -a -O--buildsystem=pybuild rm -f debian/python3-mdtraj/DEBIAN/shlibs dh_shlibdeps -a -O--buildsystem=pybuild install -m0755 -d debian/python3-mdtraj/DEBIAN dpkg-shlibdeps -Tdebian/python3-mdtraj.substvars debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_rmsd.cpython-312-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_lprmsd.cpython-312-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dtr.cpython-312-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/trr.cpython-312-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/xtc.cpython-312-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dcd.cpython-312-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighbors.cpython-312-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/drid.cpython-312-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighborlist.cpython-312-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/_geometry.cpython-312-aarch64-linux-gnu.so dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_installdeb -O--buildsystem=pybuild install -m0755 -d debian/python3-mdtraj/DEBIAN printf '#!/bin/sh\nset -e\n' > debian/python3-mdtraj/DEBIAN/postinst cat debian/python3-mdtraj.postinst.debhelper >> debian/python3-mdtraj/DEBIAN/postinst chmod 0755 -- debian/python3-mdtraj/DEBIAN/postinst printf '#!/bin/sh\nset -e\n' > debian/python3-mdtraj/DEBIAN/prerm cat debian/python3-mdtraj.prerm.debhelper >> debian/python3-mdtraj/DEBIAN/prerm chmod 0755 -- debian/python3-mdtraj/DEBIAN/prerm install -m0755 -d debian/python-mdtraj-doc/DEBIAN dh_gencontrol -O--buildsystem=pybuild install -m0755 -d debian/python3-mdtraj/DEBIAN echo misc:Depends= >> debian/python3-mdtraj.substvars echo misc:Pre-Depends= >> debian/python3-mdtraj.substvars install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/DEBIAN dpkg-gencontrol -ppython3-mdtraj -ldebian/changelog -Tdebian/python3-mdtraj.substvars -cdebian/control -Pdebian/.debhelper/python3-mdtraj/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -UProtected -UBuilt-Using -UStatic-Built-Using -DPackage=python3-mdtraj-dbgsym "-DDepends=python3-mdtraj (= \${binary:Version})" "-DDescription=debug symbols for python3-mdtraj" "-DBuild-Ids=13e77ab200d4af0076b47c5faddc43b94a9adb65 35240a209fe480e2b9f0415c22146a7e3347bc0d 4cf942d03f0949bc7ba0822d5550cb9f95142f26 6177875a14b14a42a00f3ca1801eeb87afaed36a 6b1f706f0f71d07f901a5add8ffb2c140d4a6ad0 6bb159a39c2ff605460df9153d452d2ef8ab4ac6 929d0ccd694afdabe67f7feb4a26bd7034a33eab bc92b1cc48da5dbc004c484380dedfb156445836 d4b2a93673b2221f56780e72a7e1718f0c618c5e f74789370291e76e7ca43144b1499e54431b1d15" -DSection=debug -UMulti-Arch -UReplaces -UBreaks install -m0755 -d debian/python-mdtraj-doc/DEBIAN echo misc:Depends= >> debian/python-mdtraj-doc.substvars echo misc:Pre-Depends= >> debian/python-mdtraj-doc.substvars dpkg-gencontrol -ppython-mdtraj-doc -ldebian/changelog -Tdebian/python-mdtraj-doc.substvars -cdebian/control -Pdebian/python-mdtraj-doc chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/DEBIAN/control dpkg-gencontrol -ppython3-mdtraj -ldebian/changelog -Tdebian/python3-mdtraj.substvars -cdebian/control -Pdebian/python3-mdtraj dpkg-gencontrol: warning: package python-mdtraj-doc: substitution variable ${python3:Depends} unused, but is defined dpkg-gencontrol: warning: package python-mdtraj-doc: substitution variable ${sphinxdoc:Built-Using} unused, but is defined chmod 0644 -- debian/python-mdtraj-doc/DEBIAN/control chmod 0644 -- debian/python3-mdtraj/DEBIAN/control dh_md5sums -O--buildsystem=pybuild install -m0755 -d debian/python-mdtraj-doc/DEBIAN install -m0755 -d debian/python3-mdtraj/DEBIAN cd debian/python3-mdtraj >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/python-mdtraj-doc >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/python3-mdtraj/DEBIAN/md5sums install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/DEBIAN cd debian/.debhelper/python3-mdtraj/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/python-mdtraj-doc/DEBIAN/md5sums chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/DEBIAN/md5sums dh_builddeb -O--buildsystem=pybuild dpkg-deb --root-owner-group --build debian/python3-mdtraj .. dpkg-deb --root-owner-group --build debian/python-mdtraj-doc .. dpkg-deb --root-owner-group --build debian/.debhelper/python3-mdtraj/dbgsym-root .. dpkg-deb: building package 'python-mdtraj-doc' in '../python-mdtraj-doc_1.10.1-2_all.deb'. dpkg-deb: building package 'python3-mdtraj' in '../python3-mdtraj_1.10.1-2_arm64.deb'. dpkg-deb: building package 'python3-mdtraj-dbgsym' in '../python3-mdtraj-dbgsym_1.10.1-2_arm64.deb'. dpkg-genbuildinfo --build=binary -O../mdtraj_1.10.1-2_arm64.buildinfo dpkg-genchanges --build=binary -O../mdtraj_1.10.1-2_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-source: info: using options from mdtraj-1.10.1/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: user script /srv/workspace/pbuilder/2563990/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/2563990/tmp/hooks/B01_cleanup finished 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/2563990 and its subdirectories I: Current time: Tue Dec 16 03:50:33 +14 2025 I: pbuilder-time-stamp: 1765806633