I: pbuilder: network access will be disabled during build I: Current time: Thu Sep 12 00:11:34 +14 2024 I: pbuilder-time-stamp: 1726049494 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [mdanalysis_2.7.0-5.dsc] I: copying [./mdanalysis_2.7.0.orig.tar.xz] I: copying [./mdanalysis_2.7.0-5.debian.tar.xz] I: Extracting source gpgv: Signature made Sat Aug 10 17:37:57 2024 gpgv: using RSA key 23C9A93E585819E9126D0A36573EF1E4BD5A01FA gpgv: issuer "dparsons@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./mdanalysis_2.7.0-5.dsc: no acceptable signature found dpkg-source: info: extracting mdanalysis in mdanalysis-2.7.0 dpkg-source: info: unpacking mdanalysis_2.7.0.orig.tar.xz dpkg-source: info: unpacking mdanalysis_2.7.0-5.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying docs_use_built_module.patch dpkg-source: info: applying docs_sphinx_warnings_are_not_errors.patch dpkg-source: info: applying docs_local_mathjax.patch dpkg-source: info: applying xdr_type_PR4408.patch dpkg-source: info: applying doc_no_mdanalysis_sphinx.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1520/tmp/hooks/D01_modify_environment starting debug: Running on virt64z. 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 Sep 11 10:11 /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/1520/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/1520/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]="arm-unknown-linux-gnueabihf") 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=armhf DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4 ' DIRSTACK=() DISTRIBUTION=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=arm HOST_ARCH=armhf IFS=' ' INVOCATION_ID=10804d170faf4c07b397d93ec0914625 LANG=C LANGUAGE=it_CH:it LC_ALL=C MACHTYPE=arm-unknown-linux-gnueabihf MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnueabihf 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=1520 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.i1zQlaqm/pbuilderrc_tnX1 --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.i1zQlaqm/b2 --logfile b2/build.log mdanalysis_2.7.0-5.dsc' SUDO_GID=110 SUDO_UID=103 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://10.0.0.15:3142/ I: uname -a Linux i-capture-the-hostname 6.1.0-25-arm64 #1 SMP Debian 6.1.106-3 (2024-08-26) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1520/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: armhf 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), cython3, dh-sequence-python3, pybuild-plugin-pyproject, python3-all-dev, python3-setuptools, python3-numpy, python3-biopython (>= 1.80), python3-networkx, python3-griddataformats, python3-mmtf, python3-joblib, python3-scipy, python3-matplotlib, python3-mda-xdrlib, python3-tqdm, python3-threadpoolctl, python3-packaging, python3-fasteners, python3-gsd (>= 3.0.1~), python3-netcdf4, python3-h5py, python3-seaborn, python3-sklearn, python3-duecredit, python3-hypothesis, python3-pytest, python3-sphinx, python3-msmb-theme, python3-pybtex, python3-sphinx-rtd-theme, python3-sphinx-sitemap, python3-sphinxcontrib.bibtex, libjs-mathjax dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19492 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 cython3; however: Package cython3 is not installed. pbuilder-satisfydepends-dummy depends on dh-sequence-python3; however: Package dh-sequence-python3 is not installed. pbuilder-satisfydepends-dummy depends on pybuild-plugin-pyproject; however: Package pybuild-plugin-pyproject 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-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-numpy; however: Package python3-numpy is not installed. pbuilder-satisfydepends-dummy depends on python3-biopython (>= 1.80); however: Package python3-biopython is not installed. pbuilder-satisfydepends-dummy depends on python3-networkx; however: Package python3-networkx is not installed. pbuilder-satisfydepends-dummy depends on python3-griddataformats; however: Package python3-griddataformats is not installed. pbuilder-satisfydepends-dummy depends on python3-mmtf; however: Package python3-mmtf is not installed. pbuilder-satisfydepends-dummy depends on python3-joblib; however: Package python3-joblib is not installed. pbuilder-satisfydepends-dummy depends on python3-scipy; however: Package python3-scipy is not installed. pbuilder-satisfydepends-dummy depends on python3-matplotlib; however: Package python3-matplotlib is not installed. pbuilder-satisfydepends-dummy depends on python3-mda-xdrlib; however: Package python3-mda-xdrlib is not installed. pbuilder-satisfydepends-dummy depends on python3-tqdm; however: Package python3-tqdm is not installed. pbuilder-satisfydepends-dummy depends on python3-threadpoolctl; however: Package python3-threadpoolctl is not installed. pbuilder-satisfydepends-dummy depends on python3-packaging; however: Package python3-packaging is not installed. pbuilder-satisfydepends-dummy depends on python3-fasteners; however: Package python3-fasteners is not installed. pbuilder-satisfydepends-dummy depends on python3-gsd (>= 3.0.1~); however: Package python3-gsd is not installed. pbuilder-satisfydepends-dummy depends on python3-netcdf4; however: Package python3-netcdf4 is not installed. pbuilder-satisfydepends-dummy depends on python3-h5py; however: Package python3-h5py is not installed. pbuilder-satisfydepends-dummy depends on python3-seaborn; however: Package python3-seaborn is not installed. pbuilder-satisfydepends-dummy depends on python3-sklearn; however: Package python3-sklearn is not installed. pbuilder-satisfydepends-dummy depends on python3-duecredit; however: Package python3-duecredit is not installed. pbuilder-satisfydepends-dummy depends on python3-hypothesis; however: Package python3-hypothesis is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest; however: Package python3-pytest is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx; however: Package python3-sphinx 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-pybtex; however: Package python3-pybtex is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx-rtd-theme; however: Package python3-sphinx-rtd-theme is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx-sitemap; however: Package python3-sphinx-sitemap is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinxcontrib.bibtex; however: Package python3-sphinxcontrib.bibtex is not installed. pbuilder-satisfydepends-dummy depends on libjs-mathjax; however: Package libjs-mathjax 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} fonts-urw-base35{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libaec0{a} libarchive-zip-perl{a} libblas3{a} libbrotli1{a} libcairo2{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4t64{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfontenc1{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-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} liblzf1{a} libmagic-mgc{a} libmagic1t64{a} libnetcdf19t64{a} libnghttp2-14{a} libnghttp3-9{a} libngtcp2-16{a} libngtcp2-crypto-gnutls8{a} libnsl2{a} libopenjp2-7{a} libpipeline1{a} libpixman-1-0{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} 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} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxft2{a} libxml2{a} libxrender1{a} libxslt1.1{a} libxss1{a} libyaml-0-2{a} m4{a} man-db{a} media-types{a} netbase{a} openssl{a} po-debconf{a} procps{a} pybuild-plugin-pyproject{a} python-babel-localedata{a} python-matplotlib-data{a} python3{a} python3-alabaster{a} python3-all{a} python3-all-dev{a} python3-appdirs{a} python3-attr{a} python3-babel{a} python3-biopython{a} python3-brotli{a} python3-build{a} python3-cairo{a} python3-certifi{a} python3-cftime{a} python3-chardet{a} python3-charset-normalizer{a} python3-citeproc{a} python3-contourpy{a} python3-cycler{a} python3-dateutil{a} python3-decorator{a} python3-defusedxml{a} python3-dev{a} python3-docutils{a} python3-duecredit{a} python3-fasteners{a} python3-fonttools{a} python3-freetype{a} python3-fs{a} python3-griddataformats{a} python3-gsd{a} python3-h5py{a} python3-h5py-serial{a} python3-hypothesis{a} python3-idna{a} python3-imagesize{a} python3-iniconfig{a} python3-installer{a} python3-jinja2{a} python3-joblib{a} python3-kiwisolver{a} python3-latexcodec{a} python3-looseversion{a} python3-lxml{a} python3-lz4{a} python3-markupsafe{a} python3-matplotlib{a} python3-mda-xdrlib{a} python3-minimal{a} python3-mmtf{a} python3-monotonic{a} python3-mpmath{a} python3-mrcfile{a} python3-msgpack{a} python3-msmb-theme{a} python3-netcdf4{a} python3-networkx{a} python3-numpy{a} python3-packaging{a} python3-pandas{a} python3-pandas-lib{a} python3-pil{a} python3-pil.imagetk{a} python3-pkg-resources{a} python3-pluggy{a} python3-pybtex{a} python3-pybtex-docutils{a} python3-pygments{a} python3-pyparsing{a} python3-pyproject-hooks{a} python3-pytest{a} python3-reportlab{a} python3-requests{a} python3-rlpycairo{a} python3-roman{a} python3-scipy{a} python3-seaborn{a} python3-setuptools{a} python3-six{a} python3-sklearn{a} python3-sklearn-lib{a} python3-snowballstemmer{a} python3-sortedcontainers{a} python3-sphinx{a} python3-sphinx-rtd-theme{a} python3-sphinx-sitemap{a} python3-sphinxcontrib.bibtex{a} python3-sphinxcontrib.jquery{a} python3-sympy{a} python3-threadpoolctl{a} python3-tk{a} python3-toml{a} python3-tqdm{a} python3-tz{a} python3-ufolib2{a} python3-urllib3{a} python3-wheel{a} python3-yaml{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} unicode-data{a} w3c-sgml-lib{a} x11-common{a} xfonts-encodings{a} xfonts-utils{a} xml-core{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl fonts-dejavu-extra isympy-common javascript-common krb5-locales libarchive-cpio-perl libglib2.0-data libjson-xs-perl libldap-common libltdl-dev libmail-sendmail-perl libpaper-utils libsasl2-modules linux-sysctl-defaults lynx ncbi-blast+ psmisc publicsuffix python-biopython-doc python3-bottleneck python3-bs4 python3-click python3-cssselect python3-gdal python3-html5lib python3-numexpr python3-odf python3-olefile python3-openpyxl python3-psutil python3-pydot python3-pygraphviz python3-simplejson python3-tables shared-mime-info wget xdg-user-dirs 0 packages upgraded, 252 newly installed, 0 to remove and 0 not upgraded. Need to get 169 MB of archives. After unpacking 672 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main armhf fonts-lato all 2.015-1 [2780 kB] Get: 2 http://deb.debian.org/debian trixie/main armhf libpython3.12-minimal armhf 3.12.6-1 [800 kB] Get: 3 http://deb.debian.org/debian trixie/main armhf libexpat1 armhf 2.6.3-1 [83.2 kB] Get: 4 http://deb.debian.org/debian trixie/main armhf python3.12-minimal armhf 3.12.6-1 [1812 kB] Get: 5 http://deb.debian.org/debian trixie/main armhf python3-minimal armhf 3.12.5-1 [26.7 kB] Get: 6 http://deb.debian.org/debian trixie/main armhf media-types all 10.1.0 [26.9 kB] Get: 7 http://deb.debian.org/debian trixie/main armhf netbase all 6.4 [12.8 kB] Get: 8 http://deb.debian.org/debian trixie/main armhf tzdata all 2024a-4 [255 kB] Get: 9 http://deb.debian.org/debian trixie/main armhf libkrb5support0 armhf 1.21.3-3 [30.0 kB] Get: 10 http://deb.debian.org/debian trixie/main armhf libcom-err2 armhf 1.47.1-1 [22.1 kB] Get: 11 http://deb.debian.org/debian trixie/main armhf libk5crypto3 armhf 1.21.3-3 [75.8 kB] Get: 12 http://deb.debian.org/debian trixie/main armhf libkeyutils1 armhf 1.6.3-3 [7908 B] Get: 13 http://deb.debian.org/debian trixie/main armhf libkrb5-3 armhf 1.21.3-3 [283 kB] Get: 14 http://deb.debian.org/debian trixie/main armhf libgssapi-krb5-2 armhf 1.21.3-3 [114 kB] Get: 15 http://deb.debian.org/debian trixie/main armhf libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 16 http://deb.debian.org/debian trixie/main armhf libtirpc3t64 armhf 1.3.4+ds-1.3 [71.1 kB] Get: 17 http://deb.debian.org/debian trixie/main armhf libnsl2 armhf 1.3.0-3+b2 [34.9 kB] Get: 18 http://deb.debian.org/debian trixie/main armhf readline-common all 8.2-5 [69.3 kB] Get: 19 http://deb.debian.org/debian trixie/main armhf libreadline8t64 armhf 8.2-5 [146 kB] Get: 20 http://deb.debian.org/debian trixie/main armhf libpython3.12-stdlib armhf 3.12.6-1 [1817 kB] Get: 21 http://deb.debian.org/debian trixie/main armhf python3.12 armhf 3.12.6-1 [669 kB] Get: 22 http://deb.debian.org/debian trixie/main armhf libpython3-stdlib armhf 3.12.5-1 [9584 B] Get: 23 http://deb.debian.org/debian trixie/main armhf python3 armhf 3.12.5-1 [27.6 kB] Get: 24 http://deb.debian.org/debian trixie/main armhf sgml-base all 1.31 [15.4 kB] Get: 25 http://deb.debian.org/debian trixie/main armhf libproc2-0 armhf 2:4.0.4-5 [55.8 kB] Get: 26 http://deb.debian.org/debian trixie/main armhf procps armhf 2:4.0.4-5 [863 kB] Get: 27 http://deb.debian.org/debian trixie/main armhf sensible-utils all 0.0.24 [24.8 kB] Get: 28 http://deb.debian.org/debian trixie/main armhf openssl armhf 3.3.2-1 [1348 kB] Get: 29 http://deb.debian.org/debian trixie/main armhf ca-certificates all 20240203 [158 kB] Get: 30 http://deb.debian.org/debian trixie/main armhf libmagic-mgc armhf 1:5.45-3 [314 kB] Get: 31 http://deb.debian.org/debian trixie/main armhf libmagic1t64 armhf 1:5.45-3 [98.1 kB] Get: 32 http://deb.debian.org/debian trixie/main armhf file armhf 1:5.45-3 [42.0 kB] Get: 33 http://deb.debian.org/debian trixie/main armhf gettext-base armhf 0.22.5-2 [195 kB] Get: 34 http://deb.debian.org/debian trixie/main armhf libuchardet0 armhf 0.0.8-1+b1 [65.7 kB] Get: 35 http://deb.debian.org/debian trixie/main armhf groff-base armhf 1.23.0-5 [1091 kB] Get: 36 http://deb.debian.org/debian trixie/main armhf bsdextrautils armhf 2.40.2-7 [88.6 kB] Get: 37 http://deb.debian.org/debian trixie/main armhf libpipeline1 armhf 1.5.8-1 [35.0 kB] Get: 38 http://deb.debian.org/debian trixie/main armhf man-db armhf 2.13.0-1 [1382 kB] Get: 39 http://deb.debian.org/debian trixie/main armhf m4 armhf 1.4.19-4 [264 kB] Get: 40 http://deb.debian.org/debian trixie/main armhf autoconf all 2.72-3 [493 kB] Get: 41 http://deb.debian.org/debian trixie/main armhf autotools-dev all 20220109.1 [51.6 kB] Get: 42 http://deb.debian.org/debian trixie/main armhf automake all 1:1.16.5-1.3 [823 kB] Get: 43 http://deb.debian.org/debian trixie/main armhf autopoint all 0.22.5-2 [723 kB] Get: 44 http://deb.debian.org/debian trixie/main armhf libtcl8.6 armhf 8.6.14+dfsg-1 [928 kB] Get: 45 http://deb.debian.org/debian trixie/main armhf libbrotli1 armhf 1.1.0-2+b4 [293 kB] Get: 46 http://deb.debian.org/debian trixie/main armhf libpng16-16t64 armhf 1.6.43-5 [262 kB] Get: 47 http://deb.debian.org/debian trixie/main armhf libfreetype6 armhf 2.13.3+dfsg-1 [385 kB] Get: 48 http://deb.debian.org/debian trixie/main armhf fonts-dejavu-mono all 2.37-8 [489 kB] Get: 49 http://deb.debian.org/debian trixie/main armhf fonts-dejavu-core all 2.37-8 [840 kB] Get: 50 http://deb.debian.org/debian trixie/main armhf libfontenc1 armhf 1:1.1.8-1 [20.6 kB] Get: 51 http://deb.debian.org/debian trixie/main armhf x11-common all 1:7.7+23.1 [216 kB] Get: 52 http://deb.debian.org/debian trixie/main armhf xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 53 http://deb.debian.org/debian trixie/main armhf xfonts-utils armhf 1:7.7+6 [84.5 kB] Get: 54 http://deb.debian.org/debian trixie/main armhf fonts-urw-base35 all 20200910-8 [10.8 MB] Get: 55 http://deb.debian.org/debian trixie/main armhf fontconfig-config armhf 2.15.0-1.1 [317 kB] Get: 56 http://deb.debian.org/debian trixie/main armhf libfontconfig1 armhf 2.15.0-1.1 [370 kB] Get: 57 http://deb.debian.org/debian trixie/main armhf libxau6 armhf 1:1.0.9-1+b1 [17.4 kB] Get: 58 http://deb.debian.org/debian trixie/main armhf libxdmcp6 armhf 1:1.1.2-3+b1 [23.0 kB] Get: 59 http://deb.debian.org/debian trixie/main armhf libxcb1 armhf 1.17.0-2 [140 kB] Get: 60 http://deb.debian.org/debian trixie/main armhf libx11-data all 2:1.8.7-1 [328 kB] Get: 61 http://deb.debian.org/debian trixie/main armhf libx11-6 armhf 2:1.8.7-1+b1 [739 kB] Get: 62 http://deb.debian.org/debian trixie/main armhf libxrender1 armhf 1:0.9.10-1.1+b1 [24.9 kB] Get: 63 http://deb.debian.org/debian trixie/main armhf libxft2 armhf 2.3.6-1+b1 [46.4 kB] Get: 64 http://deb.debian.org/debian trixie/main armhf libxext6 armhf 2:1.3.4-1+b1 [47.8 kB] Get: 65 http://deb.debian.org/debian trixie/main armhf libxss1 armhf 1:1.2.3-1+b1 [16.4 kB] Get: 66 http://deb.debian.org/debian trixie/main armhf libtk8.6 armhf 8.6.14-1 [693 kB] Get: 67 http://deb.debian.org/debian trixie/main armhf tk8.6-blt2.5 armhf 2.5.3+dfsg-7 [481 kB] Get: 68 http://deb.debian.org/debian trixie/main armhf blt armhf 2.5.3+dfsg-7 [6024 B] Get: 69 http://deb.debian.org/debian trixie/main armhf cython3 armhf 3.0.11+dfsg-1 [2265 kB] Get: 70 http://deb.debian.org/debian trixie/main armhf libdebhelper-perl all 13.20 [89.7 kB] Get: 71 http://deb.debian.org/debian trixie/main armhf libtool all 2.4.7-7 [517 kB] Get: 72 http://deb.debian.org/debian trixie/main armhf dh-autoreconf all 20 [17.1 kB] Get: 73 http://deb.debian.org/debian trixie/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 74 http://deb.debian.org/debian trixie/main armhf libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 75 http://deb.debian.org/debian trixie/main armhf dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 76 http://deb.debian.org/debian trixie/main armhf libelf1t64 armhf 0.191-2 [183 kB] Get: 77 http://deb.debian.org/debian trixie/main armhf dwz armhf 0.15-1+b2 [106 kB] Get: 78 http://deb.debian.org/debian trixie/main armhf libicu72 armhf 72.1-5 [9075 kB] Get: 79 http://deb.debian.org/debian trixie/main armhf libxml2 armhf 2.9.14+dfsg-1.3+b3 [598 kB] Get: 80 http://deb.debian.org/debian trixie/main armhf gettext armhf 0.22.5-2 [1485 kB] Get: 81 http://deb.debian.org/debian trixie/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 82 http://deb.debian.org/debian trixie/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 83 http://deb.debian.org/debian trixie/main armhf debhelper all 13.20 [915 kB] Get: 84 http://deb.debian.org/debian trixie/main armhf python3-pkg-resources all 70.3.0-2 [264 kB] Get: 85 http://deb.debian.org/debian trixie/main armhf python3-setuptools all 70.3.0-2 [504 kB] Get: 86 http://deb.debian.org/debian trixie/main armhf dh-python all 6.20240824 [109 kB] Get: 87 http://deb.debian.org/debian trixie/main armhf xml-core all 0.19 [20.1 kB] Get: 88 http://deb.debian.org/debian trixie/main armhf docutils-common all 0.21.2+dfsg-2 [128 kB] Get: 89 http://deb.debian.org/debian trixie/main armhf fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [517 kB] Get: 90 http://deb.debian.org/debian trixie/main armhf fonts-lyx all 2.4.1-2 [189 kB] Get: 91 http://deb.debian.org/debian trixie/main armhf fonts-mathjax all 2.7.9+dfsg-1 [2210 kB] Get: 92 http://deb.debian.org/debian trixie/main armhf libaec0 armhf 1.1.3-1 [21.5 kB] Get: 93 http://deb.debian.org/debian trixie/main armhf libblas3 armhf 3.12.0-3 [108 kB] Get: 94 http://deb.debian.org/debian trixie/main armhf libpixman-1-0 armhf 0.42.2-1+b1 [476 kB] Get: 95 http://deb.debian.org/debian trixie/main armhf libxcb-render0 armhf 1.17.0-2 [114 kB] Get: 96 http://deb.debian.org/debian trixie/main armhf libxcb-shm0 armhf 1.17.0-2 [105 kB] Get: 97 http://deb.debian.org/debian trixie/main armhf libcairo2 armhf 1.18.2-1 [443 kB] Get: 98 http://deb.debian.org/debian trixie/main armhf libsasl2-modules-db armhf 2.1.28+dfsg1-8 [18.2 kB] Get: 99 http://deb.debian.org/debian trixie/main armhf libsasl2-2 armhf 2.1.28+dfsg1-8 [50.2 kB] Get: 100 http://deb.debian.org/debian trixie/main armhf libldap-2.5-0 armhf 2.5.18+dfsg-3 [163 kB] Get: 101 http://deb.debian.org/debian trixie/main armhf libnghttp2-14 armhf 1.63.0-1 [62.9 kB] Get: 102 http://deb.debian.org/debian trixie/main armhf libnghttp3-9 armhf 1.4.0-1 [55.1 kB] Get: 103 http://deb.debian.org/debian trixie/main armhf libngtcp2-16 armhf 1.6.0-1 [118 kB] Get: 104 http://deb.debian.org/debian trixie/main armhf libngtcp2-crypto-gnutls8 armhf 1.6.0-1 [17.1 kB] Get: 105 http://deb.debian.org/debian trixie/main armhf libpsl5t64 armhf 0.21.2-1.1 [55.6 kB] Get: 106 http://deb.debian.org/debian trixie/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b4 [53.2 kB] Get: 107 http://deb.debian.org/debian trixie/main armhf libssh2-1t64 armhf 1.11.0-7 [199 kB] Get: 108 http://deb.debian.org/debian trixie/main armhf libcurl3t64-gnutls armhf 8.9.1-2 [422 kB] Get: 109 http://deb.debian.org/debian trixie/main armhf libcurl4t64 armhf 8.9.1-2 [416 kB] Get: 110 http://deb.debian.org/debian trixie/main armhf libdeflate0 armhf 1.21-1 [36.3 kB] Get: 111 http://deb.debian.org/debian trixie/main armhf libexpat1-dev armhf 2.6.3-1 [139 kB] Get: 112 http://deb.debian.org/debian trixie/main armhf libfribidi0 armhf 1.0.15-1 [70.0 kB] Get: 113 http://deb.debian.org/debian trixie/main armhf libgfortran5 armhf 14.2.0-3 [262 kB] Get: 114 http://deb.debian.org/debian trixie/main armhf libglib2.0-0t64 armhf 2.82.0-1 [1323 kB] Get: 115 http://deb.debian.org/debian trixie/main armhf libgraphite2-3 armhf 1.3.14-2 [63.2 kB] Get: 116 http://deb.debian.org/debian trixie/main armhf libharfbuzz0b armhf 9.0.0-1 [417 kB] Get: 117 http://deb.debian.org/debian trixie/main armhf libsz2 armhf 1.1.3-1 [7724 B] Get: 118 http://deb.debian.org/debian trixie/main armhf libhdf5-103-1t64 armhf 1.10.10+repack-4 [1196 kB] Get: 119 http://deb.debian.org/debian trixie/main armhf libhdf5-hl-100t64 armhf 1.10.10+repack-4 [62.3 kB] Get: 120 http://deb.debian.org/debian trixie/main armhf libimagequant0 armhf 2.18.0-1+b1 [30.7 kB] Get: 121 http://deb.debian.org/debian trixie/main armhf libjbig0 armhf 2.1-6.1+b1 [27.3 kB] Get: 122 http://deb.debian.org/debian trixie/main armhf libjpeg62-turbo armhf 1:2.1.5-3 [143 kB] Get: 123 http://deb.debian.org/debian trixie/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 124 http://deb.debian.org/debian trixie/main armhf libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 125 http://deb.debian.org/debian trixie/main armhf libjs-mathjax all 2.7.9+dfsg-1 [5667 kB] Get: 126 http://deb.debian.org/debian trixie/main armhf libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 127 http://deb.debian.org/debian trixie/main armhf libjs-sphinxdoc all 7.4.7-3 [158 kB] Get: 128 http://deb.debian.org/debian trixie/main armhf libjson-perl all 4.10000-1 [87.5 kB] Get: 129 http://deb.debian.org/debian trixie/main armhf liblapack3 armhf 3.12.0-3 [1803 kB] Get: 130 http://deb.debian.org/debian trixie/main armhf liblbfgsb0 armhf 3.0+dfsg.4-1+b1 [25.5 kB] Get: 131 http://deb.debian.org/debian trixie/main armhf liblcms2-2 armhf 2.14-2+b1 [126 kB] Get: 132 http://deb.debian.org/debian trixie/main armhf liblerc4 armhf 4.0.0+ds-4+b1 [137 kB] Get: 133 http://deb.debian.org/debian trixie/main armhf liblzf1 armhf 3.6-4+b1 [9476 B] Get: 134 http://deb.debian.org/debian trixie/main armhf libnetcdf19t64 armhf 1:4.9.2-7 [421 kB] Get: 135 http://deb.debian.org/debian trixie/main armhf libopenjp2-7 armhf 2.5.0-2+b3 [170 kB] Get: 136 http://deb.debian.org/debian trixie/main armhf libpython3.12t64 armhf 3.12.6-1 [1847 kB] Get: 137 http://deb.debian.org/debian trixie/main armhf zlib1g-dev armhf 1:1.3.dfsg+really1.3.1-1 [904 kB] Get: 138 http://deb.debian.org/debian trixie/main armhf libpython3.12-dev armhf 3.12.6-1 [3809 kB] Get: 139 http://deb.debian.org/debian trixie/main armhf libpython3-dev armhf 3.12.5-1 [9824 B] Get: 140 http://deb.debian.org/debian trixie/main armhf libpython3-all-dev armhf 3.12.5-1 [1068 B] Get: 141 http://deb.debian.org/debian trixie/main armhf libqhull-r8.0 armhf 2020.2-6+b1 [219 kB] Get: 142 http://deb.debian.org/debian trixie/main armhf libraqm0 armhf 0.10.1-1+b1 [11.8 kB] Get: 143 http://deb.debian.org/debian trixie/main armhf libsharpyuv0 armhf 1.4.0-0.1 [111 kB] Get: 144 http://deb.debian.org/debian trixie/main armhf libwebp7 armhf 1.4.0-0.1 [265 kB] Get: 145 http://deb.debian.org/debian trixie/main armhf libtiff6 armhf 4.5.1+git230720-5 [302 kB] Get: 146 http://deb.debian.org/debian trixie/main armhf libwebpdemux2 armhf 1.4.0-0.1 [110 kB] Get: 147 http://deb.debian.org/debian trixie/main armhf libwebpmux3 armhf 1.4.0-0.1 [120 kB] Get: 148 http://deb.debian.org/debian trixie/main armhf libxslt1.1 armhf 1.1.35-1.1 [212 kB] Get: 149 http://deb.debian.org/debian trixie/main armhf libyaml-0-2 armhf 0.2.5-1+b1 [45.5 kB] Get: 150 http://deb.debian.org/debian trixie/main armhf python3-packaging all 24.1-1 [45.8 kB] Get: 151 http://deb.debian.org/debian trixie/main armhf python3-pyproject-hooks all 1.1.0-2 [11.3 kB] Get: 152 http://deb.debian.org/debian trixie/main armhf python3-toml all 0.10.2-1 [16.2 kB] Get: 153 http://deb.debian.org/debian trixie/main armhf python3-wheel all 0.44.0-2 [53.4 kB] Get: 154 http://deb.debian.org/debian trixie/main armhf python3-build all 1.2.1-1 [34.1 kB] Get: 155 http://deb.debian.org/debian trixie/main armhf python3-installer all 0.7.0+dfsg1-3 [18.6 kB] Get: 156 http://deb.debian.org/debian trixie/main armhf pybuild-plugin-pyproject all 6.20240824 [11.2 kB] Get: 157 http://deb.debian.org/debian trixie/main armhf python-babel-localedata all 2.14.0-1 [5701 kB] Get: 158 http://deb.debian.org/debian trixie/main armhf python-matplotlib-data all 3.8.3-3 [2731 kB] Get: 159 http://deb.debian.org/debian trixie/main armhf python3-alabaster all 0.7.16-0.1 [27.9 kB] Get: 160 http://deb.debian.org/debian trixie/main armhf python3-all armhf 3.12.5-1 [1044 B] Get: 161 http://deb.debian.org/debian trixie/main armhf python3.12-dev armhf 3.12.6-1 [506 kB] Get: 162 http://deb.debian.org/debian trixie/main armhf python3-dev armhf 3.12.5-1 [26.2 kB] Get: 163 http://deb.debian.org/debian trixie/main armhf python3-all-dev armhf 3.12.5-1 [1068 B] Get: 164 http://deb.debian.org/debian trixie/main armhf python3-appdirs all 1.4.4-4 [12.5 kB] Get: 165 http://deb.debian.org/debian trixie/main armhf python3-attr all 23.2.0-2 [65.5 kB] Get: 166 http://deb.debian.org/debian trixie/main armhf python3-tz all 2024.1-2 [30.9 kB] Get: 167 http://deb.debian.org/debian trixie/main armhf python3-babel all 2.14.0-1 [111 kB] Get: 168 http://deb.debian.org/debian trixie/main armhf python3-numpy armhf 1:1.26.4+ds-11 [3340 kB] Get: 169 http://deb.debian.org/debian trixie/main armhf python3-chardet all 5.2.0+dfsg-1 [107 kB] Get: 170 http://deb.debian.org/debian trixie/main armhf python3.12-tk armhf 3.12.6-1 [109 kB] Get: 171 http://deb.debian.org/debian trixie/main armhf python3.13-tk armhf 3.13.0~rc2-1 [99.4 kB] Get: 172 http://deb.debian.org/debian trixie/main armhf python3-tk armhf 3.12.5-3 [9412 B] Get: 173 http://deb.debian.org/debian trixie/main armhf python3-pil.imagetk armhf 10.4.0-1 [78.8 kB] Get: 174 http://deb.debian.org/debian trixie/main armhf python3-pil armhf 10.4.0-1 [465 kB] Get: 175 http://deb.debian.org/debian trixie/main armhf python3-cairo armhf 1.26.1-1+b1 [108 kB] Get: 176 http://deb.debian.org/debian trixie/main armhf python3-freetype all 2.4.0-2 [78.6 kB] Get: 177 http://deb.debian.org/debian trixie/main armhf python3-rlpycairo all 0.3.0-3 [9904 B] Get: 178 http://deb.debian.org/debian trixie/main armhf python3-reportlab all 4.2.2-1 [1150 kB] Get: 179 http://deb.debian.org/debian trixie/main armhf w3c-sgml-lib all 1.3-3 [273 kB] Get: 180 http://deb.debian.org/debian trixie/main armhf python3-biopython armhf 1.83+dfsg1-4 [1581 kB] Get: 181 http://deb.debian.org/debian trixie/main armhf python3-brotli armhf 1.1.0-2+b4 [303 kB] Get: 182 http://deb.debian.org/debian trixie/main armhf python3-certifi all 2024.6.2-1 [157 kB] Get: 183 http://deb.debian.org/debian trixie/main armhf python3-cftime armhf 1.6.4-1+b1 [184 kB] Get: 184 http://deb.debian.org/debian trixie/main armhf python3-charset-normalizer armhf 3.3.2-2 [108 kB] Get: 185 http://deb.debian.org/debian trixie/main armhf python3-lxml armhf 5.3.0-1 [1152 kB] Get: 186 http://deb.debian.org/debian trixie/main armhf python3-citeproc all 0.6.0-3 [96.7 kB] Get: 187 http://deb.debian.org/debian trixie/main armhf python3-contourpy armhf 1.3.0-1 [178 kB] Get: 188 http://deb.debian.org/debian trixie/main armhf python3-cycler all 0.12.1-1 [9496 B] Get: 189 http://deb.debian.org/debian trixie/main armhf python3-six all 1.16.0-7 [16.4 kB] Get: 190 http://deb.debian.org/debian trixie/main armhf python3-dateutil all 2.9.0-2 [79.4 kB] Get: 191 http://deb.debian.org/debian trixie/main armhf python3-decorator all 5.1.1-5 [15.1 kB] Get: 192 http://deb.debian.org/debian trixie/main armhf python3-defusedxml all 0.7.1-2 [43.3 kB] Get: 193 http://deb.debian.org/debian trixie/main armhf python3-roman all 3.3-3 [9880 B] Get: 194 http://deb.debian.org/debian trixie/main armhf python3-docutils all 0.21.2+dfsg-2 [403 kB] Get: 195 http://deb.debian.org/debian trixie/main armhf python3-looseversion all 1.3.0-3 [8964 B] Get: 196 http://deb.debian.org/debian trixie/main armhf python3-idna all 3.6-2.1 [38.6 kB] Get: 197 http://deb.debian.org/debian trixie/main armhf python3-urllib3 all 2.0.7-2 [111 kB] Get: 198 http://deb.debian.org/debian trixie/main armhf python3-requests all 2.32.3+dfsg-1 [71.9 kB] Get: 199 http://deb.debian.org/debian trixie/main armhf python3-duecredit all 0.10.2-1 [70.4 kB] Get: 200 http://deb.debian.org/debian trixie/main armhf python3-monotonic all 1.6-2 [5728 B] Get: 201 http://deb.debian.org/debian trixie/main armhf python3-fasteners all 0.18-2 [14.0 kB] Get: 202 http://deb.debian.org/debian trixie/main armhf python3-scipy armhf 1.13.1-5 [15.2 MB] Get: 203 http://deb.debian.org/debian trixie/main armhf python3-ufolib2 all 0.16.0+dfsg1-1 [32.9 kB] Get: 204 http://deb.debian.org/debian trixie/main armhf python3-mpmath all 1.3.0-1 [419 kB] Get: 205 http://deb.debian.org/debian trixie/main armhf python3-sympy all 1.12.1-1 [3869 kB] Get: 206 http://deb.debian.org/debian trixie/main armhf python3-fs all 2.4.16-4 [95.4 kB] Get: 207 http://deb.debian.org/debian trixie/main armhf python3-lz4 armhf 4.0.2+dfsg-1+b4 [23.4 kB] Get: 208 http://deb.debian.org/debian trixie/main armhf unicode-data all 15.1.0-1 [8547 kB] Get: 209 http://deb.debian.org/debian trixie/main armhf python3-fonttools armhf 4.46.0-1+b1 [1336 kB] Get: 210 http://deb.debian.org/debian trixie/main armhf sphinx-rtd-theme-common all 2.0.0+dfsg-2 [1021 kB] Get: 211 http://deb.debian.org/debian trixie/main armhf python3-mrcfile all 1.4.3-3 [113 kB] Get: 212 http://deb.debian.org/debian trixie/main armhf python3-griddataformats all 1.0.2-2 [2048 kB] Get: 213 http://deb.debian.org/debian trixie/main armhf python3-gsd armhf 3.3.0-1+b1 [192 kB] Get: 214 http://deb.debian.org/debian trixie/main armhf python3-h5py-serial armhf 3.11.0-5 [900 kB] Get: 215 http://deb.debian.org/debian trixie/main armhf python3-h5py all 3.11.0-5 [14.7 kB] Get: 216 http://deb.debian.org/debian trixie/main armhf python3-sortedcontainers all 2.4.0-2 [31.9 kB] Get: 217 http://deb.debian.org/debian trixie/main armhf python3-hypothesis all 6.111.2-1 [320 kB] Get: 218 http://deb.debian.org/debian trixie/main armhf python3-imagesize all 1.4.1-1 [6688 B] Get: 219 http://deb.debian.org/debian trixie/main armhf python3-iniconfig all 1.1.1-2 [6396 B] Get: 220 http://deb.debian.org/debian trixie/main armhf python3-markupsafe armhf 2.1.5-1+b1 [13.2 kB] Get: 221 http://deb.debian.org/debian trixie/main armhf python3-jinja2 all 3.1.3-1 [119 kB] Get: 222 http://deb.debian.org/debian trixie/main armhf python3-joblib all 1.3.2-2 [218 kB] Get: 223 http://deb.debian.org/debian trixie/main armhf python3-kiwisolver armhf 1.4.5-1+b1 [52.9 kB] Get: 224 http://deb.debian.org/debian trixie/main armhf python3-latexcodec all 3.0.0-1 [17.5 kB] Get: 225 http://deb.debian.org/debian trixie/main armhf python3-pyparsing all 3.1.2-1 [146 kB] Get: 226 http://deb.debian.org/debian trixie/main armhf python3-matplotlib armhf 3.8.3-3 [5500 kB] Get: 227 http://deb.debian.org/debian trixie/main armhf python3-mda-xdrlib all 0.2.0-3 [11.6 kB] Get: 228 http://deb.debian.org/debian trixie/main armhf python3-msgpack armhf 1.0.3-3+b2 [74.8 kB] Get: 229 http://deb.debian.org/debian trixie/main armhf python3-mmtf all 1.1.3-1 [17.0 kB] Get: 230 http://deb.debian.org/debian trixie/main armhf sphinx-common all 7.4.7-3 [731 kB] Get: 231 http://deb.debian.org/debian trixie/main armhf python3-pygments all 2.18.0+dfsg-1 [836 kB] Get: 232 http://deb.debian.org/debian trixie/main armhf python3-snowballstemmer all 2.2.0-4 [58.0 kB] Get: 233 http://deb.debian.org/debian trixie/main armhf python3-sphinx all 7.4.7-3 [588 kB] Get: 234 http://deb.debian.org/debian trixie/main armhf python3-sphinxcontrib.jquery all 4.1-5 [7348 B] Get: 235 http://deb.debian.org/debian trixie/main armhf python3-sphinx-rtd-theme all 2.0.0+dfsg-2 [28.5 kB] Get: 236 http://deb.debian.org/debian trixie/main armhf python3-msmb-theme all 1.2.0-4 [33.8 kB] Get: 237 http://deb.debian.org/debian trixie/main armhf python3-netcdf4 armhf 1.7.1-1+b1 [529 kB] Get: 238 http://deb.debian.org/debian trixie/main armhf python3-networkx all 3.2.1-4 [14.2 MB] Get: 239 http://deb.debian.org/debian trixie/main armhf python3-pandas-lib armhf 2.2.2+dfsg-4+b1 [3773 kB] Get: 240 http://deb.debian.org/debian trixie/main armhf python3-pandas all 2.2.2+dfsg-4 [3095 kB] Get: 241 http://deb.debian.org/debian trixie/main armhf python3-pluggy all 1.5.0-1 [26.9 kB] Get: 242 http://deb.debian.org/debian trixie/main armhf python3-yaml armhf 6.0.2-1 [123 kB] Get: 243 http://deb.debian.org/debian trixie/main armhf python3-pybtex all 0.24.0-4 [74.6 kB] Get: 244 http://deb.debian.org/debian trixie/main armhf python3-pybtex-docutils all 1.0.2-1 [8064 B] Get: 245 http://deb.debian.org/debian trixie/main armhf python3-pytest all 8.3.2-1 [249 kB] Get: 246 http://deb.debian.org/debian trixie/main armhf python3-seaborn all 0.13.2-4 [215 kB] Get: 247 http://deb.debian.org/debian trixie/main armhf python3-threadpoolctl all 3.1.0-1 [21.2 kB] Get: 248 http://deb.debian.org/debian trixie/main armhf python3-sklearn-lib armhf 1.4.2+dfsg-6 [3163 kB] Get: 249 http://deb.debian.org/debian trixie/main armhf python3-sklearn all 1.4.2+dfsg-6 [2248 kB] Get: 250 http://deb.debian.org/debian trixie/main armhf python3-sphinx-sitemap all 2.6.0-1 [8508 B] Get: 251 http://deb.debian.org/debian trixie/main armhf python3-sphinxcontrib.bibtex all 2.6.2-1 [32.4 kB] Get: 252 http://deb.debian.org/debian trixie/main armhf python3-tqdm all 4.66.5-1 [90.1 kB] Fetched 169 MB in 21s (8234 kB/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 ... 19492 files and directories currently installed.) Preparing to unpack .../fonts-lato_2.015-1_all.deb ... Unpacking fonts-lato (2.015-1) ... Selecting previously unselected package libpython3.12-minimal:armhf. Preparing to unpack .../libpython3.12-minimal_3.12.6-1_armhf.deb ... Unpacking libpython3.12-minimal:armhf (3.12.6-1) ... Selecting previously unselected package libexpat1:armhf. 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Selecting previously unselected package libgssapi-krb5-2:armhf. Preparing to unpack .../09-libgssapi-krb5-2_1.21.3-3_armhf.deb ... Unpacking libgssapi-krb5-2:armhf (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:armhf. Preparing to unpack .../11-libtirpc3t64_1.3.4+ds-1.3_armhf.deb ... Adding 'diversion of /lib/arm-linux-gnueabihf/libtirpc.so.3 to /lib/arm-linux-gnueabihf/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/arm-linux-gnueabihf/libtirpc.so.3.0.0 to /lib/arm-linux-gnueabihf/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:armhf (1.3.4+ds-1.3) ... Selecting previously unselected package libnsl2:armhf. Preparing to unpack .../12-libnsl2_1.3.0-3+b2_armhf.deb ... Unpacking libnsl2:armhf (1.3.0-3+b2) ... 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:armhf. Preparing to unpack .../14-libreadline8t64_8.2-5_armhf.deb ... Adding 'diversion of /lib/arm-linux-gnueabihf/libhistory.so.8 to /lib/arm-linux-gnueabihf/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/arm-linux-gnueabihf/libhistory.so.8.2 to /lib/arm-linux-gnueabihf/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/arm-linux-gnueabihf/libreadline.so.8 to /lib/arm-linux-gnueabihf/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/arm-linux-gnueabihf/libreadline.so.8.2 to /lib/arm-linux-gnueabihf/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:armhf (8.2-5) ... Selecting previously unselected package libpython3.12-stdlib:armhf. Preparing to unpack .../15-libpython3.12-stdlib_3.12.6-1_armhf.deb ... Unpacking libpython3.12-stdlib:armhf (3.12.6-1) ... Selecting previously unselected package python3.12. Preparing to unpack .../16-python3.12_3.12.6-1_armhf.deb ... Unpacking python3.12 (3.12.6-1) ... Selecting previously unselected package libpython3-stdlib:armhf. Preparing to unpack .../17-libpython3-stdlib_3.12.5-1_armhf.deb ... Unpacking libpython3-stdlib:armhf (3.12.5-1) ... Setting up python3-minimal (3.12.5-1) ... Selecting previously unselected package python3. (Reading database ... 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Preparing to unpack .../009-file_1%3a5.45-3_armhf.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../010-gettext-base_0.22.5-2_armhf.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../011-libuchardet0_0.0.8-1+b1_armhf.deb ... Unpacking libuchardet0:armhf (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../012-groff-base_1.23.0-5_armhf.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../013-bsdextrautils_2.40.2-7_armhf.deb ... Unpacking bsdextrautils (2.40.2-7) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../014-libpipeline1_1.5.8-1_armhf.deb ... Unpacking libpipeline1:armhf (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../015-man-db_2.13.0-1_armhf.deb ... 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Selecting previously unselected package x11-common. Preparing to unpack .../028-x11-common_1%3a7.7+23.1_all.deb ... Unpacking x11-common (1:7.7+23.1) ... Selecting previously unselected package xfonts-encodings. Preparing to unpack .../029-xfonts-encodings_1%3a1.0.4-2.2_all.deb ... Unpacking xfonts-encodings (1:1.0.4-2.2) ... Selecting previously unselected package xfonts-utils. Preparing to unpack .../030-xfonts-utils_1%3a7.7+6_armhf.deb ... Unpacking xfonts-utils (1:7.7+6) ... Selecting previously unselected package fonts-urw-base35. Preparing to unpack .../031-fonts-urw-base35_20200910-8_all.deb ... Unpacking fonts-urw-base35 (20200910-8) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../032-fontconfig-config_2.15.0-1.1_armhf.deb ... Unpacking fontconfig-config (2.15.0-1.1) ... Selecting previously unselected package libfontconfig1:armhf. Preparing to unpack .../033-libfontconfig1_2.15.0-1.1_armhf.deb ... Unpacking libfontconfig1:armhf (2.15.0-1.1) ... Selecting previously unselected package libxau6:armhf. Preparing to unpack .../034-libxau6_1%3a1.0.9-1+b1_armhf.deb ... Unpacking libxau6:armhf (1:1.0.9-1+b1) ... Selecting previously unselected package libxdmcp6:armhf. Preparing to unpack .../035-libxdmcp6_1%3a1.1.2-3+b1_armhf.deb ... Unpacking libxdmcp6:armhf (1:1.1.2-3+b1) ... Selecting previously unselected package libxcb1:armhf. Preparing to unpack .../036-libxcb1_1.17.0-2_armhf.deb ... Unpacking libxcb1:armhf (1.17.0-2) ... Selecting previously unselected package libx11-data. Preparing to unpack .../037-libx11-data_2%3a1.8.7-1_all.deb ... Unpacking libx11-data (2:1.8.7-1) ... Selecting previously unselected package libx11-6:armhf. Preparing to unpack .../038-libx11-6_2%3a1.8.7-1+b1_armhf.deb ... Unpacking libx11-6:armhf (2:1.8.7-1+b1) ... Selecting previously unselected package libxrender1:armhf. Preparing to unpack .../039-libxrender1_1%3a0.9.10-1.1+b1_armhf.deb ... Unpacking libxrender1:armhf (1:0.9.10-1.1+b1) ... Selecting previously unselected package libxft2:armhf. Preparing to unpack .../040-libxft2_2.3.6-1+b1_armhf.deb ... Unpacking libxft2:armhf (2.3.6-1+b1) ... Selecting previously unselected package libxext6:armhf. Preparing to unpack .../041-libxext6_2%3a1.3.4-1+b1_armhf.deb ... Unpacking libxext6:armhf (2:1.3.4-1+b1) ... Selecting previously unselected package libxss1:armhf. Preparing to unpack .../042-libxss1_1%3a1.2.3-1+b1_armhf.deb ... Unpacking libxss1:armhf (1:1.2.3-1+b1) ... Selecting previously unselected package libtk8.6:armhf. Preparing to unpack .../043-libtk8.6_8.6.14-1_armhf.deb ... Unpacking libtk8.6:armhf (8.6.14-1) ... Selecting previously unselected package tk8.6-blt2.5. Preparing to unpack .../044-tk8.6-blt2.5_2.5.3+dfsg-7_armhf.deb ... Unpacking tk8.6-blt2.5 (2.5.3+dfsg-7) ... Selecting previously unselected package blt. Preparing to unpack .../045-blt_2.5.3+dfsg-7_armhf.deb ... Unpacking blt (2.5.3+dfsg-7) ... Selecting previously unselected package cython3. Preparing to unpack .../046-cython3_3.0.11+dfsg-1_armhf.deb ... Unpacking cython3 (3.0.11+dfsg-1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../047-libdebhelper-perl_13.20_all.deb ... Unpacking libdebhelper-perl (13.20) ... Selecting previously unselected package libtool. Preparing to unpack .../048-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../049-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../050-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../051-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../052-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... Selecting previously unselected package libelf1t64:armhf. Preparing to unpack .../053-libelf1t64_0.191-2_armhf.deb ... Unpacking libelf1t64:armhf (0.191-2) ... Selecting previously unselected package dwz. Preparing to unpack .../054-dwz_0.15-1+b2_armhf.deb ... Unpacking dwz (0.15-1+b2) ... Selecting previously unselected package libicu72:armhf. Preparing to unpack .../055-libicu72_72.1-5_armhf.deb ... Unpacking libicu72:armhf (72.1-5) ... Selecting previously unselected package libxml2:armhf. Preparing to unpack .../056-libxml2_2.9.14+dfsg-1.3+b3_armhf.deb ... Unpacking libxml2:armhf (2.9.14+dfsg-1.3+b3) ... Selecting previously unselected package gettext. Preparing to unpack .../057-gettext_0.22.5-2_armhf.deb ... Unpacking gettext (0.22.5-2) ... 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Setting up libpipeline1:armhf (1.5.8-1) ... Setting up libgraphite2-3:armhf (1.3.14-2) ... Setting up liblcms2-2:armhf (2.14-2+b1) ... Setting up libpixman-1-0:armhf (0.42.2-1+b1) ... Setting up libsharpyuv0:armhf (1.4.0-0.1) ... Setting up libxau6:armhf (1:1.0.9-1+b1) ... Setting up libxdmcp6:armhf (1:1.1.2-3+b1) ... Setting up libkeyutils1:armhf (1.6.3-3) ... Setting up libxcb1:armhf (1.17.0-2) ... Setting up fonts-lato (2.015-1) ... Setting up fonts-mathjax (2.7.9+dfsg-1) ... Setting up libicu72:armhf (72.1-5) ... Setting up liblerc4:armhf (4.0.0+ds-4+b1) ... Setting up bsdextrautils (2.40.2-7) ... Setting up libjs-mathjax (2.7.9+dfsg-1) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libxcb-render0:armhf (1.17.0-2) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libyaml-0-2:armhf (0.2.5-1+b1) ... Setting up libtirpc-common (1.3.4+ds-1.3) ... Setting up fonts-lyx (2.4.1-2) ... Setting up libdebhelper-perl (13.20) ... Setting up libbrotli1:armhf (1.1.0-2+b4) ... Setting up libmagic1t64:armhf (1:5.45-3) ... 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:armhf (0.21.2-1.1) ... Setting up libnghttp2-14:armhf (1.63.0-1) ... Setting up libdeflate0:armhf (1.21-1) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up libqhull-r8.0:armhf (2020.2-6+b1) ... Setting up libxcb-shm0:armhf (1.17.0-2) ... Setting up libcom-err2:armhf (1.47.1-1) ... Setting up file (1:5.45-3) ... Setting up libjbig0:armhf (2.1-6.1+b1) ... Setting up libaec0:armhf (1.1.3-1) ... Setting up libelf1t64:armhf (0.191-2) ... Setting up python-babel-localedata (2.14.0-1) ... Setting up libkrb5support0:armhf (1.21.3-3) ... Setting up libsasl2-modules-db:armhf (2.1.28+dfsg1-8) ... Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' Local time is now: Wed Sep 11 10:12:57 UTC 2024. Universal Time is now: Wed Sep 11 10:12:57 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up unicode-data (15.1.0-1) ... Setting up libfontenc1:armhf (1:1.1.8-1) ... Setting up autotools-dev (20220109.1) ... Setting up libglib2.0-0t64:armhf (2.82.0-1) ... No schema files found: doing nothing. Setting up libblas3:armhf (3.12.0-3) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode Setting up libexpat1-dev:armhf (2.6.3-1) ... Setting up libjpeg62-turbo:armhf (1:2.1.5-3) ... Setting up libx11-data (2:1.8.7-1) ... Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b4) ... Setting up liblzf1:armhf (3.6-4+b1) ... Setting up xfonts-encodings (1:1.0.4-2.2) ... Setting up libfribidi0:armhf (1.0.15-1) ... Setting up libimagequant0:armhf (2.18.0-1+b1) ... Setting up libproc2-0:armhf (2:4.0.4-5) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:armhf (1.6.43-5) ... Setting up libtcl8.6:armhf (8.6.14+dfsg-1) ... Setting up autopoint (0.22.5-2) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libk5crypto3:armhf (1.21.3-3) ... Setting up libsasl2-2:armhf (2.1.28+dfsg1-8) ... Setting up libgfortran5:armhf (14.2.0-3) ... Setting up autoconf (2.72-3) ... Setting up libnghttp3-9:armhf (1.4.0-1) ... Setting up libwebp7:armhf (1.4.0-0.1) ... Setting up zlib1g-dev:armhf (1:1.3.dfsg+really1.3.1-1) ... Setting up dwz (0.15-1+b2) ... Setting up sensible-utils (0.0.24) ... Setting up libtiff6:armhf (4.5.1+git230720-5) ... Setting up libuchardet0:armhf (0.0.8-1+b1) ... Setting up procps (2:4.0.4-5) ... Setting up libjson-perl (4.10000-1) ... Setting up libopenjp2-7:armhf (2.5.0-2+b3) ... Setting up libx11-6:armhf (2:1.8.7-1+b1) ... Setting up netbase (6.4) ... Setting up libngtcp2-16:armhf (1.6.0-1) ... Setting up sgml-base (1.31) ... Setting up libkrb5-3:armhf (1.21.3-3) ... Setting up libssh2-1t64:armhf (1.11.0-7) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up python-matplotlib-data (3.8.3-3) ... Setting up openssl (3.3.2-1) ... Setting up libwebpmux3:armhf (1.4.0-0.1) ... Setting up readline-common (8.2-5) ... Setting up libxml2:armhf (2.9.14+dfsg-1.3+b3) ... Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... Setting up sphinx-rtd-theme-common (2.0.0+dfsg-2) ... Setting up libngtcp2-crypto-gnutls8:armhf (1.6.0-1) ... Setting up libsz2:armhf (1.1.3-1) ... 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:armhf (3.12.0-3) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode Setting up gettext (0.22.5-2) ... Setting up libxrender1:armhf (1:0.9.10-1.1+b1) ... Setting up libtool (2.4.7-7) ... Setting up fontconfig-config (2.15.0-1.1) ... Setting up libwebpdemux2:armhf (1.4.0-0.1) ... Setting up libxext6:armhf (2:1.3.4-1+b1) ... Setting up libldap-2.5-0:armhf (2.5.18+dfsg-3) ... 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 libfreetype6:armhf (2.13.3+dfsg-1) ... Setting up libgssapi-krb5-2:armhf (1.21.3-3) ... Setting up libjs-sphinxdoc (7.4.7-3) ... Setting up libreadline8t64:armhf (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:armhf (1.1.35-1.1) ... Setting up libharfbuzz0b:armhf (9.0.0-1) ... Setting up libxss1:armhf (1:1.2.3-1+b1) ... Setting up libfontconfig1:armhf (2.15.0-1.1) ... Setting up liblbfgsb0:armhf (3.0+dfsg.4-1+b1) ... Setting up libxft2:armhf (2.3.6-1+b1) ... Setting up libcurl4t64:armhf (8.9.1-2) ... Setting up libtirpc3t64:armhf (1.3.4+ds-1.3) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libtk8.6:armhf (8.6.14-1) ... Setting up python3.12-tk (3.12.6-1) ... Setting up libcurl3t64-gnutls:armhf (8.9.1-2) ... Setting up xfonts-utils (1:7.7+6) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libcairo2:armhf (1.18.2-1) ... Setting up python3.13-tk (3.13.0~rc2-1) ... Setting up libraqm0:armhf (0.10.1-1+b1) ... Setting up sphinx-common (7.4.7-3) ... Setting up libnsl2:armhf (1.3.0-3+b2) ... Setting up libhdf5-103-1t64:armhf (1.10.10+repack-4) ... Setting up libhdf5-hl-100t64:armhf (1.10.10+repack-4) ... Setting up tk8.6-blt2.5 (2.5.3+dfsg-7) ... Setting up libnetcdf19t64:armhf (1:4.9.2-7) ... Setting up libpython3.12-stdlib:armhf (3.12.6-1) ... Setting up blt (2.5.3+dfsg-7) ... Setting up python3.12 (3.12.6-1) ... Setting up debhelper (13.20) ... Setting up fonts-urw-base35 (20200910-8) ... Setting up libpython3.12t64:armhf (3.12.6-1) ... Setting up libpython3-stdlib:armhf (3.12.5-1) ... Setting up python3 (3.12.5-1) ... Setting up libpython3.12-dev:armhf (3.12.6-1) ... Setting up python3-sortedcontainers (2.4.0-2) ... Setting up python3-freetype (2.4.0-2) ... Setting up python3-markupsafe (2.1.5-1+b1) ... Setting up python3-wheel (0.44.0-2) ... Setting up python3-mda-xdrlib (0.2.0-3) ... Setting up python3-tz (2024.1-2) ... Setting up python3-monotonic (1.6-2) ... Setting up python3-six (1.16.0-7) ... Setting up python3-pil:armhf (10.4.0-1) ... Setting up python3-roman (3.3-3) ... Setting up python3-decorator (5.1.1-5) ... Setting up python3-jinja2 (3.1.3-1) ... Setting up python3-packaging (24.1-1) ... Setting up python3-pyproject-hooks (1.1.0-2) ... Setting up python3-pyparsing (3.1.2-1) ... Setting up python3-certifi (2024.6.2-1) ... Setting up python3-snowballstemmer (2.2.0-4) ... Setting up python3-brotli (1.1.0-2+b4) ... Setting up python3-cycler (0.12.1-1) ... Setting up python3-kiwisolver (1.4.5-1+b1) ... Setting up python3-idna (3.6-2.1) ... Setting up python3.12-dev (3.12.6-1) ... Setting up cython3 (3.0.11+dfsg-1) ... Setting up python3-fasteners (0.18-2) ... Setting up python3-toml (0.10.2-1) ... Setting up python3-installer (0.7.0+dfsg1-3) ... Setting up python3-urllib3 (2.0.7-2) ... Setting up python3-pluggy (1.5.0-1) ... Setting up python3-looseversion (1.3.0-3) ... Setting up python3-lxml:armhf (5.3.0-1) ... Setting up python3-dateutil (2.9.0-2) ... Setting up python3-msgpack (1.0.3-3+b2) ... Setting up python3-mpmath (1.3.0-1) ... Setting up python3-build (1.2.1-1) ... Setting up python3-appdirs (1.4.4-4) ... Setting up python3-imagesize (1.4.1-1) ... Setting up python3-pkg-resources (70.3.0-2) ... Setting up python3-iniconfig (1.1.1-2) ... Setting up python3-sympy (1.12.1-1) ... Setting up python3-attr (23.2.0-2) ... Setting up libpython3-dev:armhf (3.12.5-1) ... Setting up python3-cairo (1.26.1-1+b1) ... Setting up python3-setuptools (70.3.0-2) ... Setting up python3-joblib (1.3.2-2) ... 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-lz4 (4.0.2+dfsg-1+b4) ... Setting up python3-defusedxml (0.7.1-2) ... Setting up python3-citeproc (0.6.0-3) ... Setting up python3-charset-normalizer (3.3.2-2) ... Setting up python3-pytest (8.3.2-1) ... Setting up python3-alabaster (0.7.16-0.1) ... Setting up python3-hypothesis (6.111.2-1) ... Setting up python3-tqdm (4.66.5-1) ... Setting up python3-threadpoolctl (3.1.0-1) ... Setting up python3-latexcodec (3.0.0-1) ... Setting up python3-all (3.12.5-1) ... Setting up python3-yaml (6.0.2-1) ... Setting up python3-tk:armhf (3.12.5-3) ... 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-pil.imagetk:armhf (10.4.0-1) ... Setting up python3-rlpycairo (0.3.0-3) ... Setting up libpython3-all-dev:armhf (3.12.5-1) ... Setting up python3-dev (3.12.5-1) ... Setting up python3-requests (2.32.3+dfsg-1) ... Setting up python3-numpy (1:1.26.4+ds-11) ... Setting up python3-reportlab (4.2.2-1) ... Setting up python3-pybtex (0.24.0-4) ... Setting up python3-contourpy (1.3.0-1) ... Setting up python3-mrcfile (1.4.3-3) ... Setting up dh-python (6.20240824) ... Setting up python3-all-dev (3.12.5-1) ... Setting up python3-scipy (1.13.1-5) ... Setting up python3-duecredit (0.10.2-1) ... Setting up pybuild-plugin-pyproject (6.20240824) ... Setting up python3-pandas-lib:armhf (2.2.2+dfsg-4+b1) ... Setting up python3-sklearn-lib:armhf (1.4.2+dfsg-6) ... Setting up python3-h5py-serial (3.11.0-5) ... Setting up python3-gsd (3.3.0-1+b1) ... Setting up python3-mmtf (1.1.3-1) ... Setting up python3-griddataformats (1.0.2-2) ... Setting up python3-pandas (2.2.2+dfsg-4) ... Setting up python3-h5py (3.11.0-5) ... Setting up python3-sklearn (1.4.2+dfsg-6) ... Setting up python3-cftime (1.6.4-1+b1) ... Setting up python3-netcdf4 (1.7.1-1+b1) ... Setting up python3-fonttools (4.46.0-1+b1) ... Setting up python3-ufolib2 (0.16.0+dfsg1-1) ... Setting up python3-matplotlib (3.8.3-3) ... Setting up python3-seaborn (0.13.2-4) ... Processing triggers for libc-bin (2.40-2) ... Processing triggers for sgml-base (1.31) ... Setting up docutils-common (0.21.2+dfsg-2) ... Setting up w3c-sgml-lib (1.3-3) ... Setting up python3-biopython (1.83+dfsg1-4) ... Processing triggers for sgml-base (1.31) ... Setting up python3-docutils (0.21.2+dfsg-2) ... Setting up python3-pybtex-docutils (1.0.2-1) ... Setting up python3-sphinx (7.4.7-3) ... Setting up python3-sphinxcontrib.bibtex (2.6.2-1) ... Setting up python3-sphinx-sitemap (2.6.0-1) ... Setting up python3-sphinxcontrib.jquery (4.1-5) ... Setting up python3-sphinx-rtd-theme (2.0.0+dfsg-2) ... 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/1520/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/1520/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/mdanalysis-2.7.0/ && 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 > ../mdanalysis_2.7.0-5_source.changes dpkg-buildpackage: info: source package mdanalysis dpkg-buildpackage: info: source version 2.7.0-5 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Drew Parsons dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf dpkg-source: info: using options from mdanalysis-2.7.0/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/ debian/rules clean dh clean --with sphinxdoc --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild debian/rules execute_after_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/mdanalysis-2.7.0' rm -f .duecredit.p rm -f package/MDAnalysis/authors.py rm -f package/MDAnalysis/analysis/encore/clustering/affinityprop.c \ package/MDAnalysis/analysis/encore/cutils.c \ package/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c \ package/MDAnalysis/coordinates/timestep.cpp \ package/MDAnalysis/lib/_augment.cpp \ package/MDAnalysis/lib/_cutil.cpp \ package/MDAnalysis/lib/c_distances.c \ package/MDAnalysis/lib/c_distances_openmp.c \ package/MDAnalysis/lib/formats/cython_util.c \ package/MDAnalysis/lib/formats/libdcd.c \ package/MDAnalysis/lib/formats/libmdaxdr.c \ package/MDAnalysis/lib/nsgrid.cpp \ package/MDAnalysis/lib/qcprot.c rm -rf package/MDAnalysis.egg-info rm -f testsuite/MDAnalysisTests/data/.*_offsets.npz testsuite/MDAnalysisTests/data/*/.*_offsets.npz rm -rf testsuite/.pytest_cache make[1]: Leaving directory '/build/reproducible-path/mdanalysis-2.7.0' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild 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 dh_auto_build -O--buildsystem=pybuild I: pybuild plugin_pyproject:129: Building wheel for python3.12 with "build" module I: pybuild base:311: python3.12 -m build --skip-dependency-check --no-isolation --wheel --outdir /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis * Building wheel... performance hint: MDAnalysis/lib/c_distances.pyx:275:5: Exception check on '_minimum_image_orthogonal' will always require the GIL to be acquired. Possible solutions: 1. Declare '_minimum_image_orthogonal' 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 '_minimum_image_orthogonal' to allow an error code to be returned. performance hint: MDAnalysis/lib/c_distances.pyx:302:5: Exception check on '_minimum_image_triclinic' will always require the GIL to be acquired. Possible solutions: 1. Declare '_minimum_image_triclinic' 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 '_minimum_image_triclinic' to allow an error code to be returned. performance hint: MDAnalysis/lib/c_distances.pyx:390:37: Exception check after calling '__pyx_fuse_0_minimum_image_orthogonal' will always require the GIL to be acquired. Possible solutions: 1. Declare '__pyx_fuse_0_minimum_image_orthogonal' 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 '__pyx_fuse_0_minimum_image_orthogonal' to allow an error code to be returned. performance hint: MDAnalysis/lib/c_distances.pyx:390:37: Exception check after calling '__pyx_fuse_1_minimum_image_orthogonal' will always require the GIL to be acquired. Possible solutions: 1. Declare '__pyx_fuse_1_minimum_image_orthogonal' 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 '__pyx_fuse_1_minimum_image_orthogonal' to allow an error code to be returned. performance hint: MDAnalysis/lib/c_distances.pyx:414:36: Exception check after calling '__pyx_fuse_0_minimum_image_triclinic' will always require the GIL to be acquired. Possible solutions: 1. Declare '__pyx_fuse_0_minimum_image_triclinic' 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 '__pyx_fuse_0_minimum_image_triclinic' to allow an error code to be returned. performance hint: MDAnalysis/lib/c_distances.pyx:414:36: Exception check after calling '__pyx_fuse_1_minimum_image_triclinic' will always require the GIL to be acquired. Possible solutions: 1. Declare '__pyx_fuse_1_minimum_image_triclinic' 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 '__pyx_fuse_1_minimum_image_triclinic' to allow an error code to be returned. performance hint: MDAnalysis/lib/nsgrid.pyx:417:37: Exception check after calling 'coord2cellid' will always require the GIL to be acquired. Declare 'coord2cellid' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. performance hint: MDAnalysis/lib/nsgrid.pyx:431:26: Exception check after calling 'coord2cellxyz' will always require the GIL to be acquired. Possible solutions: 1. Declare 'coord2cellxyz' 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 'coord2cellxyz' to allow an error code to be returned. performance hint: MDAnalysis/lib/nsgrid.pyx:559:34: Exception check after calling 'coord2cellxyz' will always require the GIL to be acquired. Possible solutions: 1. Declare 'coord2cellxyz' 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 'coord2cellxyz' to allow an error code to be returned. performance hint: MDAnalysis/lib/nsgrid.pyx:567:56: Exception check after calling 'cellxyz2cellid' will always require the GIL to be acquired. Declare 'cellxyz2cellid' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. performance hint: MDAnalysis/lib/nsgrid.pyx:574:53: Exception check after calling 'calc_distsq' will always require the GIL to be acquired. Declare 'calc_distsq' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. performance hint: MDAnalysis/lib/nsgrid.pyx:578:57: Exception check after calling 'add_neighbors' will always require the GIL to be acquired. Possible solutions: 1. Declare 'add_neighbors' 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 'add_neighbors' to allow an error code to be returned. Attempting to autodetect OpenMP support... Compiler supports OpenMP Will attempt to use Cython. Compiling MDAnalysis/lib/formats/libdcd.pyx because it changed. Compiling MDAnalysis/lib/c_distances.pyx because it changed. Compiling MDAnalysis/lib/c_distances_openmp.pyx because it changed. Compiling MDAnalysis/lib/qcprot.pyx because it changed. Compiling MDAnalysis/lib/formats/libmdaxdr.pyx because it changed. Compiling MDAnalysis/lib/formats/cython_util.pyx because it changed. Compiling MDAnalysis/analysis/encore/cutils.pyx because it changed. Compiling MDAnalysis/analysis/encore/clustering/affinityprop.pyx because it changed. Compiling MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx because it changed. Compiling MDAnalysis/lib/_cutil.pyx because it changed. Compiling MDAnalysis/lib/_augment.pyx because it changed. Compiling MDAnalysis/lib/nsgrid.pyx because it changed. Compiling MDAnalysis/coordinates/timestep.pyx because it changed. [ 1/13] Cythonizing MDAnalysis/analysis/encore/clustering/affinityprop.pyx [ 2/13] Cythonizing MDAnalysis/analysis/encore/cutils.pyx [ 3/13] Cythonizing MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx [ 4/13] Cythonizing MDAnalysis/coordinates/timestep.pyx [ 5/13] Cythonizing MDAnalysis/lib/_augment.pyx [ 6/13] Cythonizing MDAnalysis/lib/_cutil.pyx [ 7/13] Cythonizing MDAnalysis/lib/c_distances.pyx [ 8/13] Cythonizing MDAnalysis/lib/c_distances_openmp.pyx [ 9/13] Cythonizing MDAnalysis/lib/formats/cython_util.pyx [10/13] Cythonizing MDAnalysis/lib/formats/libdcd.pyx [11/13] Cythonizing MDAnalysis/lib/formats/libmdaxdr.pyx [12/13] Cythonizing MDAnalysis/lib/nsgrid.pyx [13/13] Cythonizing MDAnalysis/lib/qcprot.pyx /usr/lib/python3/dist-packages/setuptools/config/_apply_pyprojecttoml.py:79: SetuptoolsWarning: `install_requires` overwritten in `pyproject.toml` (dependencies) corresp(dist, value, root_dir) running bdist_wheel running build running build_py creating build creating build/lib.linux-armv7l-cpython-312 creating build/lib.linux-armv7l-cpython-312/MDAnalysis copying MDAnalysis/version.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis copying MDAnalysis/__init__.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis copying MDAnalysis/due.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis copying MDAnalysis/authors.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis copying MDAnalysis/units.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis copying MDAnalysis/exceptions.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis creating build/lib.linux-armv7l-cpython-312/MDAnalysis/core copying MDAnalysis/core/accessors.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/core copying MDAnalysis/core/topology.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/core copying MDAnalysis/core/groups.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/core copying MDAnalysis/core/__init__.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/core copying MDAnalysis/core/topologyattrs.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/core copying MDAnalysis/core/_get_readers.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/core copying MDAnalysis/core/selection.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/core copying MDAnalysis/core/topologyobjects.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/core copying MDAnalysis/core/universe.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/core creating build/lib.linux-armv7l-cpython-312/MDAnalysis/visualization copying MDAnalysis/visualization/streamlines.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/visualization copying MDAnalysis/visualization/__init__.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/visualization copying MDAnalysis/visualization/streamlines_3D.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/visualization creating build/lib.linux-armv7l-cpython-312/MDAnalysis/tests copying MDAnalysis/tests/__init__.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/tests copying MDAnalysis/tests/datafiles.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/tests creating build/lib.linux-armv7l-cpython-312/MDAnalysis/selections copying MDAnalysis/selections/jmol.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/selections copying MDAnalysis/selections/vmd.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/selections copying MDAnalysis/selections/__init__.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/selections copying MDAnalysis/selections/charmm.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/selections copying MDAnalysis/selections/pymol.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/selections copying MDAnalysis/selections/gromacs.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/selections copying MDAnalysis/selections/base.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/selections creating build/lib.linux-armv7l-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/ITPParser.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/TPRParser.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/guessers.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/HoomdXMLParser.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/GSDParser.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/PDBQTParser.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/MinimalParser.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/GMSParser.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/PQRParser.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/CRDParser.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/PSFParser.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/__init__.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/DLPolyParser.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/TOPParser.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/core.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/DMSParser.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/ExtendedPDBParser.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/ParmEdParser.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/MOL2Parser.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/GROParser.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/MMTFParser.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/XYZParser.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/PDBParser.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/FHIAIMSParser.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/TXYZParser.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/tables.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/LAMMPSParser.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/base.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/topology creating build/lib.linux-armv7l-cpython-312/MDAnalysis/converters copying MDAnalysis/converters/RDKit.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/converters copying MDAnalysis/converters/OpenMMParser.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/converters copying MDAnalysis/converters/__init__.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/converters copying MDAnalysis/converters/OpenMM.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/converters copying MDAnalysis/converters/ParmEd.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/converters copying MDAnalysis/converters/RDKitParser.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/converters copying MDAnalysis/converters/ParmEdParser.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/converters copying MDAnalysis/converters/base.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/converters creating build/lib.linux-armv7l-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/TNG.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/memory.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/XDR.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/TRJ.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/DLPoly.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/DMS.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/PDB.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/TRC.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/chemfiles.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/MMTF.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/CRD.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/GSD.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/GRO.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/__init__.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/LAMMPS.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/core.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/ParmEd.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/XTC.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/null.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/chain.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/TXYZ.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/NAMDBIN.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/XYZ.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/FHIAIMS.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/GMS.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/PQR.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/TRZ.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/H5MD.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/PDBQT.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/MOL2.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/DCD.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/TRR.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/base.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/INPCRD.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/coordinates creating build/lib.linux-armv7l-cpython-312/MDAnalysis/transformations copying MDAnalysis/transformations/positionaveraging.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/transformations copying MDAnalysis/transformations/wrap.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/transformations copying MDAnalysis/transformations/rotate.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/transformations copying MDAnalysis/transformations/__init__.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/transformations copying MDAnalysis/transformations/fit.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/transformations copying MDAnalysis/transformations/translate.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/transformations copying MDAnalysis/transformations/nojump.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/transformations copying MDAnalysis/transformations/boxdimensions.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/transformations copying MDAnalysis/transformations/base.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/transformations creating build/lib.linux-armv7l-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/log.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/correlations.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/NeighborSearch.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/distances.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/mdamath.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/picklable_file_io.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/__init__.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/_distopia.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/pkdtree.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/util.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/transformations.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/lib creating build/lib.linux-armv7l-cpython-312/MDAnalysis/auxiliary copying MDAnalysis/auxiliary/__init__.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/auxiliary copying MDAnalysis/auxiliary/core.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/auxiliary copying MDAnalysis/auxiliary/XVG.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/auxiliary copying MDAnalysis/auxiliary/EDR.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/auxiliary copying MDAnalysis/auxiliary/base.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/auxiliary creating build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/nucleicacids.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/nuclinfo.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/align.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/rdf.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/msd.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/density.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/distances.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/dihedrals.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/__init__.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/helix_analysis.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/pca.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/psa.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/polymer.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/gnm.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/waterdynamics.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/atomicdistances.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/bat.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/lineardensity.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/dielectric.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/contacts.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/leaflet.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/diffusionmap.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/rms.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/base.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis creating build/lib.linux-armv7l-cpython-312/MDAnalysis/topology/tpr copying MDAnalysis/topology/tpr/utils.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/topology/tpr copying MDAnalysis/topology/tpr/__init__.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/topology/tpr copying MDAnalysis/topology/tpr/setting.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/topology/tpr copying MDAnalysis/topology/tpr/obj.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/topology/tpr creating build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/__init__.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/formats creating build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/legacy copying MDAnalysis/analysis/legacy/__init__.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/legacy copying MDAnalysis/analysis/legacy/x3dna.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/legacy creating build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/hydrogenbonds copying MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/hydrogenbonds copying MDAnalysis/analysis/hydrogenbonds/__init__.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/hydrogenbonds copying MDAnalysis/analysis/hydrogenbonds/hbond_autocorrel.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/hydrogenbonds copying MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/hydrogenbonds creating build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/hole2 copying MDAnalysis/analysis/hole2/utils.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/hole2 copying MDAnalysis/analysis/hole2/hole.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/hole2 copying MDAnalysis/analysis/hole2/templates.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/hole2 copying MDAnalysis/analysis/hole2/__init__.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/hole2 creating build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/hbonds copying MDAnalysis/analysis/hbonds/__init__.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/hbonds copying MDAnalysis/analysis/hbonds/hbond_autocorrel.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/hbonds creating build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/data copying MDAnalysis/analysis/data/__init__.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/data copying MDAnalysis/analysis/data/filenames.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/data creating build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/utils.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/confdistmatrix.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/similarity.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/__init__.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/bootstrap.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/covariance.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/encore creating build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction copying MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction copying MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction copying MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction creating build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/encore/clustering copying MDAnalysis/analysis/encore/clustering/__init__.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/encore/clustering copying MDAnalysis/analysis/encore/clustering/cluster.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/encore/clustering copying MDAnalysis/analysis/encore/clustering/ClusteringMethod.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/encore/clustering copying MDAnalysis/analysis/encore/clustering/ClusterCollection.py -> build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/encore/clustering running egg_info creating MDAnalysis.egg-info writing MDAnalysis.egg-info/PKG-INFO writing dependency_links to MDAnalysis.egg-info/dependency_links.txt writing requirements to MDAnalysis.egg-info/requires.txt writing top-level names to MDAnalysis.egg-info/top_level.txt writing manifest file 'MDAnalysis.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 /build/reproducible-path/mdanalysis-2.7.0/package/MDAnalysis/lib/include/calc_distances.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 /build/reproducible-path/mdanalysis-2.7.0/package/MDAnalysis/lib/include/calc_distances.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 dependency /build/reproducible-path/mdanalysis-2.7.0/package/MDAnalysis/analysis/encore/clustering/include/ap.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 /build/reproducible-path/mdanalysis-2.7.0/package/MDAnalysis/analysis/encore/dimensionality_reduction/include/spe.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 /build/reproducible-path/mdanalysis-2.7.0/package/MDAnalysis/lib/include/calc_distances.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 /build/reproducible-path/mdanalysis-2.7.0/package/MDAnalysis/lib/include/calc_distances.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 'MDAnalysis.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no previously-included files matching 'doc/html/html' found anywhere in distribution warning: no previously-included files matching '*.pyc' found anywhere in distribution warning: no previously-included files matching '*.pyo' found anywhere in distribution warning: no previously-included files matching '*.pyd' found anywhere in distribution warning: no previously-included files matching '*~' found anywhere in distribution warning: no previously-included files matching '.git' found anywhere in distribution adding license file 'LICENSE' adding license file 'AUTHORS' writing manifest file 'MDAnalysis.egg-info/SOURCES.txt' /usr/lib/python3/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'MDAnalysis.analysis.encore.clustering.include' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'MDAnalysis.analysis.encore.clustering.include' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'MDAnalysis.analysis.encore.clustering.include' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'MDAnalysis.analysis.encore.clustering.include' to be distributed and are already explicitly excluding 'MDAnalysis.analysis.encore.clustering.include' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'MDAnalysis.analysis.encore.clustering.src' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'MDAnalysis.analysis.encore.clustering.src' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'MDAnalysis.analysis.encore.clustering.src' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'MDAnalysis.analysis.encore.clustering.src' to be distributed and are already explicitly excluding 'MDAnalysis.analysis.encore.clustering.src' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'MDAnalysis.analysis.encore.dimensionality_reduction.include' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'MDAnalysis.analysis.encore.dimensionality_reduction.include' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'MDAnalysis.analysis.encore.dimensionality_reduction.include' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'MDAnalysis.analysis.encore.dimensionality_reduction.include' to be distributed and are already explicitly excluding 'MDAnalysis.analysis.encore.dimensionality_reduction.include' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'MDAnalysis.analysis.encore.dimensionality_reduction.src' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'MDAnalysis.analysis.encore.dimensionality_reduction.src' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'MDAnalysis.analysis.encore.dimensionality_reduction.src' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'MDAnalysis.analysis.encore.dimensionality_reduction.src' to be distributed and are already explicitly excluding 'MDAnalysis.analysis.encore.dimensionality_reduction.src' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'MDAnalysis.lib.formats.include' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'MDAnalysis.lib.formats.include' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'MDAnalysis.lib.formats.include' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'MDAnalysis.lib.formats.include' to be distributed and are already explicitly excluding 'MDAnalysis.lib.formats.include' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'MDAnalysis.lib.formats.src' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'MDAnalysis.lib.formats.src' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'MDAnalysis.lib.formats.src' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'MDAnalysis.lib.formats.src' to be distributed and are already explicitly excluding 'MDAnalysis.lib.formats.src' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'MDAnalysis.lib.include' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'MDAnalysis.lib.include' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'MDAnalysis.lib.include' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'MDAnalysis.lib.include' to be distributed and are already explicitly excluding 'MDAnalysis.lib.include' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'MDAnalysis.lib.libmdanalysis' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'MDAnalysis.lib.libmdanalysis' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'MDAnalysis.lib.libmdanalysis' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'MDAnalysis.lib.libmdanalysis' to be distributed and are already explicitly excluding 'MDAnalysis.lib.libmdanalysis' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'MDAnalysis.lib.src.transformations' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'MDAnalysis.lib.src.transformations' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'MDAnalysis.lib.src.transformations' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'MDAnalysis.lib.src.transformations' to be distributed and are already explicitly excluding 'MDAnalysis.lib.src.transformations' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) copying MDAnalysis/analysis/data/rama_ref_data.npy -> build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/data copying MDAnalysis/analysis/data/janin_ref_data.npy -> build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/data copying MDAnalysis/coordinates/timestep.cpp -> build/lib.linux-armv7l-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/timestep.pxd -> build/lib.linux-armv7l-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/timestep.pyx -> build/lib.linux-armv7l-cpython-312/MDAnalysis/coordinates copying MDAnalysis/lib/_augment.cpp -> build/lib.linux-armv7l-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/_augment.pyx -> build/lib.linux-armv7l-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/_cutil.cpp -> build/lib.linux-armv7l-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/_cutil.pxd -> build/lib.linux-armv7l-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/_cutil.pyx -> build/lib.linux-armv7l-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/c_distances.c -> build/lib.linux-armv7l-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/c_distances.pxd -> build/lib.linux-armv7l-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/c_distances.pyx -> build/lib.linux-armv7l-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/c_distances_openmp.c -> build/lib.linux-armv7l-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/c_distances_openmp.pyx -> build/lib.linux-armv7l-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/nsgrid.cpp -> build/lib.linux-armv7l-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/nsgrid.pyx -> build/lib.linux-armv7l-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/qcprot.c -> build/lib.linux-armv7l-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/qcprot.pyx -> build/lib.linux-armv7l-cpython-312/MDAnalysis/lib creating build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/include copying MDAnalysis/lib/include/calc_distances.h -> build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/include creating build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/libmdanalysis copying MDAnalysis/lib/libmdanalysis/__init__.pxd -> build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/libmdanalysis creating build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/src creating build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/src/transformations copying MDAnalysis/lib/src/transformations/AUTHOR -> build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/src/transformations copying MDAnalysis/lib/src/transformations/LICENCE -> build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/src/transformations copying MDAnalysis/lib/src/transformations/transformations.c -> build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/src/transformations copying MDAnalysis/lib/formats/cython_util.c -> build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/cython_util.pxd -> build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/cython_util.pyx -> build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/libdcd.c -> build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/libdcd.pxd -> build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/libdcd.pyx -> build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/libmdaxdr.c -> build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/libmdaxdr.pxd -> build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/libmdaxdr.pyx -> build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/formats creating build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/endianswap.h -> build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/fastio.h -> build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/readdcd.h -> build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/trr_seek.h -> build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/xdrfile.h -> build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/xdrfile_trr.h -> build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/xdrfile_xtc.h -> build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/xtc_seek.h -> build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/formats/include creating build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/formats/src copying MDAnalysis/lib/formats/src/trr_seek.c -> build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/formats/src copying MDAnalysis/lib/formats/src/xdrfile.c -> build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/formats/src copying MDAnalysis/lib/formats/src/xdrfile_trr.c -> build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/formats/src copying MDAnalysis/lib/formats/src/xdrfile_xtc.c -> build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/formats/src copying MDAnalysis/lib/formats/src/xtc_seek.c -> build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/formats/src copying MDAnalysis/analysis/encore/cutils.c -> build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/cutils.pyx -> build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c -> build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction copying MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx -> build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction creating build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction/include copying MDAnalysis/analysis/encore/dimensionality_reduction/include/spe.h -> build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction/include creating build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction/src copying MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.c -> build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction/src copying MDAnalysis/analysis/encore/clustering/affinityprop.c -> build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/encore/clustering copying MDAnalysis/analysis/encore/clustering/affinityprop.pyx -> build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/encore/clustering creating build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/encore/clustering/include copying MDAnalysis/analysis/encore/clustering/include/ap.h -> build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/encore/clustering/include creating build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/encore/clustering/src copying MDAnalysis/analysis/encore/clustering/src/ap.c -> build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/encore/clustering/src running build_ext building 'MDAnalysis.lib.formats.libdcd' extension creating build/temp.linux-armv7l-cpython-312 creating build/temp.linux-armv7l-cpython-312/MDAnalysis creating build/temp.linux-armv7l-cpython-312/MDAnalysis/lib creating build/temp.linux-armv7l-cpython-312/MDAnalysis/lib/formats arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.7.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/mdanalysis-2.7.0/package/MDAnalysis/lib/formats -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/mdanalysis-2.7.0/package/MDAnalysis/lib/formats/include -I/usr/include/python3.12 -c MDAnalysis/lib/formats/libdcd.c -o build/temp.linux-armv7l-cpython-312/MDAnalysis/lib/formats/libdcd.o -std=c99 -O3 -funroll-loops -fsigned-zeros 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 MDAnalysis/lib/formats/libdcd.c:1261: /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 file included from MDAnalysis/lib/formats/libdcd.c:1268: MDAnalysis/lib/formats/include/readdcd.h: In function 'read_dcdstep': MDAnalysis/lib/formats/include/readdcd.h:562:21: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 562 | if (tmpbuf[i] != sizeof(float)*N) return DCD_BADFORMAT; | ^~ MDAnalysis/lib/formats/include/readdcd.h: In function 'write_dcdheader': MDAnalysis/lib/formats/include/readdcd.h:698:14: warning: unused variable 'tmbuf' [-Wunused-variable] 698 | struct tm *tmbuf; | ^~~~~ MDAnalysis/lib/formats/include/readdcd.h:697:10: warning: unused variable 'cur_time' [-Wunused-variable] 697 | time_t cur_time; | ^~~~~~~~ In file included from MDAnalysis/lib/formats/include/readdcd.h:25: MDAnalysis/lib/formats/include/endianswap.h: At top level: MDAnalysis/lib/formats/include/endianswap.h:96:13: warning: 'swap2_aligned' defined but not used [-Wunused-function] 96 | static void swap2_aligned(void *v, long ndata) { | ^~~~~~~~~~~~~ MDAnalysis/lib/formats/include/endianswap.h:32:13: warning: 'swap2_unaligned' defined but not used [-Wunused-function] 32 | static void swap2_unaligned(void *v, long ndata) { | ^~~~~~~~~~~~~~~ In file included from MDAnalysis/lib/formats/libdcd.c:1267: MDAnalysis/lib/formats/include/fastio.h:453:12: warning: 'fio_write_str' defined but not used [-Wunused-function] 453 | static int fio_write_str(fio_fd fd, const char *str) { | ^~~~~~~~~~~~~ MDAnalysis/lib/formats/include/fastio.h:449:12: warning: 'fio_read_int32' defined but not used [-Wunused-function] 449 | static int fio_read_int32(fio_fd fd, int *i) { | ^~~~~~~~~~~~~~ arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.7.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-cpython-312/MDAnalysis/lib/formats/libdcd.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/formats/libdcd.cpython-312-arm-linux-gnueabihf.so building 'MDAnalysis.lib.c_distances' extension arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.7.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/mdanalysis-2.7.0/package/MDAnalysis/lib/include -I/usr/include/python3.12 -c MDAnalysis/lib/c_distances.c -o build/temp.linux-armv7l-cpython-312/MDAnalysis/lib/c_distances.o -std=c99 -O3 -funroll-loops -fsigned-zeros 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 MDAnalysis/lib/c_distances.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 " \ | ^~~~~~~ arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.7.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-cpython-312/MDAnalysis/lib/c_distances.o -L/usr/lib/arm-linux-gnueabihf -lm -o build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/c_distances.cpython-312-arm-linux-gnueabihf.so building 'MDAnalysis.lib.c_distances_openmp' extension arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.7.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DPARALLEL -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/mdanalysis-2.7.0/package/MDAnalysis/lib/include -I/usr/include/python3.12 -c MDAnalysis/lib/c_distances_openmp.c -o build/temp.linux-armv7l-cpython-312/MDAnalysis/lib/c_distances_openmp.o -fopenmp -std=c99 -O3 -funroll-loops -fsigned-zeros 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 MDAnalysis/lib/c_distances_openmp.c:1272: /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 " \ | ^~~~~~~ arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.7.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-cpython-312/MDAnalysis/lib/c_distances_openmp.o -L/usr/lib/arm-linux-gnueabihf -lm -lgomp -o build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/c_distances_openmp.cpython-312-arm-linux-gnueabihf.so -fopenmp building 'MDAnalysis.lib.qcprot' extension arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.7.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c MDAnalysis/lib/qcprot.c -o build/temp.linux-armv7l-cpython-312/MDAnalysis/lib/qcprot.o -std=c99 -O3 -funroll-loops -fsigned-zeros 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 MDAnalysis/lib/qcprot.c:1255: /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 " \ | ^~~~~~~ MDAnalysis/lib/qcprot.c: In function '__pyx_fuse_0__pyx_f_10MDAnalysis_3lib_6qcprot_InnerProduct': MDAnalysis/lib/qcprot.c:21123:35: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 21123 | for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) { | ^ MDAnalysis/lib/qcprot.c:21331:35: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 21331 | for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) { | ^ MDAnalysis/lib/qcprot.c: In function '__pyx_fuse_1__pyx_f_10MDAnalysis_3lib_6qcprot_InnerProduct': MDAnalysis/lib/qcprot.c:21801:35: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 21801 | for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) { | ^ MDAnalysis/lib/qcprot.c:22009:35: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 22009 | for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) { | ^ arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.7.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-cpython-312/MDAnalysis/lib/qcprot.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/qcprot.cpython-312-arm-linux-gnueabihf.so building 'MDAnalysis.lib._transformations' extension creating build/temp.linux-armv7l-cpython-312/MDAnalysis/lib/src creating build/temp.linux-armv7l-cpython-312/MDAnalysis/lib/src/transformations arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.7.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c MDAnalysis/lib/src/transformations/transformations.c -o build/temp.linux-armv7l-cpython-312/MDAnalysis/lib/src/transformations/transformations.o -std=c99 -O3 -funroll-loops -fsigned-zeros 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 MDAnalysis/lib/src/transformations/transformations.c:73: /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 " \ | ^~~~~~~ MDAnalysis/lib/src/transformations/transformations.c: In function 'py_superimposition_matrix': MDAnalysis/lib/src/transformations/transformations.c:1837: warning: ignoring '#pragma vector always' [-Wunknown-pragmas] 1837 | #pragma vector always MDAnalysis/lib/src/transformations/transformations.c:1954: warning: ignoring '#pragma vector always' [-Wunknown-pragmas] 1954 | #pragma vector always MDAnalysis/lib/src/transformations/transformations.c:1978: warning: ignoring '#pragma vector always' [-Wunknown-pragmas] 1978 | #pragma vector always MDAnalysis/lib/src/transformations/transformations.c: In function 'py_vector_norm': MDAnalysis/lib/src/transformations/transformations.c:3414: warning: ignoring '#pragma vector always' [-Wunknown-pragmas] 3414 | #pragma vector always MDAnalysis/lib/src/transformations/transformations.c:3495: warning: ignoring '#pragma vector always' [-Wunknown-pragmas] 3495 | #pragma vector always MDAnalysis/lib/src/transformations/transformations.c: In function 'py_unit_vector': MDAnalysis/lib/src/transformations/transformations.c:3597: warning: ignoring '#pragma vector always' [-Wunknown-pragmas] 3597 | #pragma vector always MDAnalysis/lib/src/transformations/transformations.c:3602: warning: ignoring '#pragma vector always' [-Wunknown-pragmas] 3602 | #pragma vector always MDAnalysis/lib/src/transformations/transformations.c:3666: warning: ignoring '#pragma vector always' [-Wunknown-pragmas] 3666 | #pragma vector always MDAnalysis/lib/src/transformations/transformations.c:3671: warning: ignoring '#pragma vector always' [-Wunknown-pragmas] 3671 | #pragma vector always MDAnalysis/lib/src/transformations/transformations.c: At top level: MDAnalysis/lib/src/transformations/transformations.c:910:1: warning: 'PyConverter_DoubleVector4Copy' defined but not used [-Wunused-function] 910 | PyConverter_DoubleVector4Copy( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ MDAnalysis/lib/src/transformations/transformations.c:804:1: warning: 'PyConverter_DoubleArrayOrNone' defined but not used [-Wunused-function] 804 | PyConverter_DoubleArrayOrNone( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ MDAnalysis/lib/src/transformations/transformations.c:774:1: warning: 'PyConverter_DoubleArray' defined but not used [-Wunused-function] 774 | PyConverter_DoubleArray( | ^~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.7.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-cpython-312/MDAnalysis/lib/src/transformations/transformations.o -L/usr/lib/arm-linux-gnueabihf -lm -o build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/_transformations.cpython-312-arm-linux-gnueabihf.so building 'MDAnalysis.lib.formats.libmdaxdr' extension creating build/temp.linux-armv7l-cpython-312/MDAnalysis/lib/formats/src arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.7.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/mdanalysis-2.7.0/package/MDAnalysis/lib/formats -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/mdanalysis-2.7.0/package/MDAnalysis/lib/formats/include -I/build/reproducible-path/mdanalysis-2.7.0/package/MDAnalysis/lib/formats -I/usr/include/python3.12 -c MDAnalysis/lib/formats/libmdaxdr.c -o build/temp.linux-armv7l-cpython-312/MDAnalysis/lib/formats/libmdaxdr.o -std=c99 -O3 -funroll-loops -fsigned-zeros 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 MDAnalysis/lib/formats/libmdaxdr.c:1282: /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 file included from MDAnalysis/lib/formats/libmdaxdr.c:1288: MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- In file included from MDAnalysis/lib/formats/libmdaxdr.c:1289: MDAnalysis/lib/formats/include/xdrfile_xtc.h:5:2: warning: "/*" within comment [-Wcomment] 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- In file included from MDAnalysis/lib/formats/include/xdrfile_xtc.h:43: MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- In file included from MDAnalysis/lib/formats/libmdaxdr.c:1290: MDAnalysis/lib/formats/include/xdrfile_trr.h:5:2: warning: "/*" within comment [-Wcomment] 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.7.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/mdanalysis-2.7.0/package/MDAnalysis/lib/formats -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/mdanalysis-2.7.0/package/MDAnalysis/lib/formats/include -I/build/reproducible-path/mdanalysis-2.7.0/package/MDAnalysis/lib/formats -I/usr/include/python3.12 -c MDAnalysis/lib/formats/src/trr_seek.c -o build/temp.linux-armv7l-cpython-312/MDAnalysis/lib/formats/src/trr_seek.o -std=c99 -O3 -funroll-loops -fsigned-zeros In file included from MDAnalysis/lib/formats/src/trr_seek.c:30: /build/reproducible-path/mdanalysis-2.7.0/package/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- In file included from MDAnalysis/lib/formats/src/trr_seek.c:31: /build/reproducible-path/mdanalysis-2.7.0/package/MDAnalysis/lib/formats/include/xdrfile_trr.h:5:2: warning: "/*" within comment [-Wcomment] 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- In file included from /build/reproducible-path/mdanalysis-2.7.0/package/MDAnalysis/lib/formats/include/xdrfile_trr.h:42: /build/reproducible-path/mdanalysis-2.7.0/package/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- MDAnalysis/lib/formats/src/trr_seek.c: In function 'read_trr_n_frames': MDAnalysis/lib/formats/src/trr_seek.c:39:27: warning: unused variable 'totalframebytes' [-Wunused-variable] 39 | int result, framebytes, totalframebytes; | ^~~~~~~~~~~~~~~ MDAnalysis/lib/formats/src/trr_seek.c:38:15: warning: unused variable 'lambda' [-Wunused-variable] 38 | float time, lambda; | ^~~~~~ MDAnalysis/lib/formats/src/trr_seek.c:38:9: warning: unused variable 'time' [-Wunused-variable] 38 | float time, lambda; | ^~~~ arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.7.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/mdanalysis-2.7.0/package/MDAnalysis/lib/formats -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/mdanalysis-2.7.0/package/MDAnalysis/lib/formats/include -I/build/reproducible-path/mdanalysis-2.7.0/package/MDAnalysis/lib/formats -I/usr/include/python3.12 -c MDAnalysis/lib/formats/src/xdrfile.c -o build/temp.linux-armv7l-cpython-312/MDAnalysis/lib/formats/src/xdrfile.o -std=c99 -O3 -funroll-loops -fsigned-zeros In file included from MDAnalysis/lib/formats/src/xdrfile.c:62: /build/reproducible-path/mdanalysis-2.7.0/package/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- MDAnalysis/lib/formats/src/xdrfile.c: In function 'sizeofint': MDAnalysis/lib/formats/src/xdrfile.c:501:17: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 501 | while (size >= num && num_of_bits < 32) | ^~ MDAnalysis/lib/formats/src/xdrfile.c: In function 'sizeofints': MDAnalysis/lib/formats/src/xdrfile.c:547:32: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 547 | while (bytes[num_of_bytes] >= num) | ^~ MDAnalysis/lib/formats/src/xdrfile.c: In function 'encodeints': MDAnalysis/lib/formats/src/xdrfile.c:656:21: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 656 | if (num_of_bits >= num_of_bytes * 8) | ^~ MDAnalysis/lib/formats/src/xdrfile.c:658:31: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 658 | for (i = 0; i < num_of_bytes; i++) | ^ MDAnalysis/lib/formats/src/xdrfile.c:666:31: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 666 | for (i = 0; i < num_of_bytes-1; i++) | ^ MDAnalysis/lib/formats/src/xdrfile.c: In function 'decodebits': MDAnalysis/lib/formats/src/xdrfile.c:706:30: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 706 | if (lastbits < num_of_bits) | ^ MDAnalysis/lib/formats/src/xdrfile.c: In function 'xdrfile_decompress_coord_float': MDAnalysis/lib/formats/src/xdrfile.c:816:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 816 | if(size3>xfp->buf1size) | ^ MDAnalysis/lib/formats/src/xdrfile.c:868:26: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 868 | maxidx = (LASTIDXxfp->buf1size) | ^ MDAnalysis/lib/formats/src/xdrfile.c:1135:25: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 1135 | while (smallidx < LASTIDX && magicints[smallidx] < mindiff) | ^ MDAnalysis/lib/formats/src/xdrfile.c:1141:26: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 1141 | maxidx = (LASTIDXxfp->buf1size) | ^ MDAnalysis/lib/formats/src/xdrfile.c:1368:26: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 1368 | maxidx = (LASTIDXxfp->buf1size) { | ^ MDAnalysis/lib/formats/src/xdrfile.c:1619:25: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 1619 | while (smallidx < LASTIDX && magicints[smallidx] < mindiff) { | ^ MDAnalysis/lib/formats/src/xdrfile.c:1624:26: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 1624 | maxidx = (LASTIDX build/bdist.linux-armv7l/wheel/MDAnalysis creating build/bdist.linux-armv7l/wheel/MDAnalysis/core copying build/lib.linux-armv7l-cpython-312/MDAnalysis/core/accessors.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core copying build/lib.linux-armv7l-cpython-312/MDAnalysis/core/topology.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core copying build/lib.linux-armv7l-cpython-312/MDAnalysis/core/groups.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core copying build/lib.linux-armv7l-cpython-312/MDAnalysis/core/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core copying build/lib.linux-armv7l-cpython-312/MDAnalysis/core/topologyattrs.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core copying build/lib.linux-armv7l-cpython-312/MDAnalysis/core/_get_readers.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core copying build/lib.linux-armv7l-cpython-312/MDAnalysis/core/selection.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core copying build/lib.linux-armv7l-cpython-312/MDAnalysis/core/topologyobjects.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core copying build/lib.linux-armv7l-cpython-312/MDAnalysis/core/universe.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core creating build/bdist.linux-armv7l/wheel/MDAnalysis/visualization copying build/lib.linux-armv7l-cpython-312/MDAnalysis/visualization/streamlines.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/visualization copying build/lib.linux-armv7l-cpython-312/MDAnalysis/visualization/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/visualization copying build/lib.linux-armv7l-cpython-312/MDAnalysis/visualization/streamlines_3D.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/visualization creating build/bdist.linux-armv7l/wheel/MDAnalysis/tests copying build/lib.linux-armv7l-cpython-312/MDAnalysis/tests/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/tests copying build/lib.linux-armv7l-cpython-312/MDAnalysis/tests/datafiles.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/tests creating build/bdist.linux-armv7l/wheel/MDAnalysis/selections copying build/lib.linux-armv7l-cpython-312/MDAnalysis/selections/jmol.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/selections copying build/lib.linux-armv7l-cpython-312/MDAnalysis/selections/vmd.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/selections copying build/lib.linux-armv7l-cpython-312/MDAnalysis/selections/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/selections copying build/lib.linux-armv7l-cpython-312/MDAnalysis/selections/charmm.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/selections copying build/lib.linux-armv7l-cpython-312/MDAnalysis/selections/pymol.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/selections copying build/lib.linux-armv7l-cpython-312/MDAnalysis/selections/gromacs.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/selections copying build/lib.linux-armv7l-cpython-312/MDAnalysis/selections/base.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/selections creating build/bdist.linux-armv7l/wheel/MDAnalysis/topology copying build/lib.linux-armv7l-cpython-312/MDAnalysis/topology/ITPParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology copying build/lib.linux-armv7l-cpython-312/MDAnalysis/topology/TPRParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology copying build/lib.linux-armv7l-cpython-312/MDAnalysis/topology/guessers.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology copying build/lib.linux-armv7l-cpython-312/MDAnalysis/topology/HoomdXMLParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology copying build/lib.linux-armv7l-cpython-312/MDAnalysis/topology/GSDParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology copying build/lib.linux-armv7l-cpython-312/MDAnalysis/topology/PDBQTParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology copying build/lib.linux-armv7l-cpython-312/MDAnalysis/topology/MinimalParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology copying build/lib.linux-armv7l-cpython-312/MDAnalysis/topology/GMSParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology copying build/lib.linux-armv7l-cpython-312/MDAnalysis/topology/PQRParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology copying build/lib.linux-armv7l-cpython-312/MDAnalysis/topology/CRDParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology copying build/lib.linux-armv7l-cpython-312/MDAnalysis/topology/PSFParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology copying build/lib.linux-armv7l-cpython-312/MDAnalysis/topology/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology copying build/lib.linux-armv7l-cpython-312/MDAnalysis/topology/DLPolyParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology copying build/lib.linux-armv7l-cpython-312/MDAnalysis/topology/TOPParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology creating build/bdist.linux-armv7l/wheel/MDAnalysis/topology/tpr copying build/lib.linux-armv7l-cpython-312/MDAnalysis/topology/tpr/utils.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology/tpr copying build/lib.linux-armv7l-cpython-312/MDAnalysis/topology/tpr/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology/tpr copying build/lib.linux-armv7l-cpython-312/MDAnalysis/topology/tpr/setting.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology/tpr copying build/lib.linux-armv7l-cpython-312/MDAnalysis/topology/tpr/obj.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology/tpr copying build/lib.linux-armv7l-cpython-312/MDAnalysis/topology/core.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology copying build/lib.linux-armv7l-cpython-312/MDAnalysis/topology/DMSParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology copying build/lib.linux-armv7l-cpython-312/MDAnalysis/topology/ExtendedPDBParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology copying build/lib.linux-armv7l-cpython-312/MDAnalysis/topology/ParmEdParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology copying build/lib.linux-armv7l-cpython-312/MDAnalysis/topology/MOL2Parser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology copying build/lib.linux-armv7l-cpython-312/MDAnalysis/topology/GROParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology copying build/lib.linux-armv7l-cpython-312/MDAnalysis/topology/MMTFParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology copying build/lib.linux-armv7l-cpython-312/MDAnalysis/topology/XYZParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology copying build/lib.linux-armv7l-cpython-312/MDAnalysis/topology/PDBParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology copying build/lib.linux-armv7l-cpython-312/MDAnalysis/topology/FHIAIMSParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology copying build/lib.linux-armv7l-cpython-312/MDAnalysis/topology/TXYZParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology copying build/lib.linux-armv7l-cpython-312/MDAnalysis/topology/tables.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology copying build/lib.linux-armv7l-cpython-312/MDAnalysis/topology/LAMMPSParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology copying build/lib.linux-armv7l-cpython-312/MDAnalysis/topology/base.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology copying build/lib.linux-armv7l-cpython-312/MDAnalysis/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis copying build/lib.linux-armv7l-cpython-312/MDAnalysis/due.py -> build/bdist.linux-armv7l/wheel/MDAnalysis creating build/bdist.linux-armv7l/wheel/MDAnalysis/converters copying build/lib.linux-armv7l-cpython-312/MDAnalysis/converters/RDKit.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/converters copying build/lib.linux-armv7l-cpython-312/MDAnalysis/converters/OpenMMParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/converters copying build/lib.linux-armv7l-cpython-312/MDAnalysis/converters/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/converters copying build/lib.linux-armv7l-cpython-312/MDAnalysis/converters/OpenMM.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/converters copying build/lib.linux-armv7l-cpython-312/MDAnalysis/converters/ParmEd.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/converters copying build/lib.linux-armv7l-cpython-312/MDAnalysis/converters/RDKitParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/converters copying build/lib.linux-armv7l-cpython-312/MDAnalysis/converters/ParmEdParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/converters copying build/lib.linux-armv7l-cpython-312/MDAnalysis/converters/base.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/converters creating build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates copying build/lib.linux-armv7l-cpython-312/MDAnalysis/coordinates/TNG.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates copying build/lib.linux-armv7l-cpython-312/MDAnalysis/coordinates/memory.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates copying build/lib.linux-armv7l-cpython-312/MDAnalysis/coordinates/XDR.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates copying build/lib.linux-armv7l-cpython-312/MDAnalysis/coordinates/TRJ.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates copying build/lib.linux-armv7l-cpython-312/MDAnalysis/coordinates/DLPoly.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates copying build/lib.linux-armv7l-cpython-312/MDAnalysis/coordinates/DMS.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates copying build/lib.linux-armv7l-cpython-312/MDAnalysis/coordinates/PDB.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates copying build/lib.linux-armv7l-cpython-312/MDAnalysis/coordinates/TRC.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates copying build/lib.linux-armv7l-cpython-312/MDAnalysis/coordinates/chemfiles.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates copying build/lib.linux-armv7l-cpython-312/MDAnalysis/coordinates/MMTF.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates copying build/lib.linux-armv7l-cpython-312/MDAnalysis/coordinates/CRD.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates copying build/lib.linux-armv7l-cpython-312/MDAnalysis/coordinates/GSD.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates copying build/lib.linux-armv7l-cpython-312/MDAnalysis/coordinates/GRO.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates copying build/lib.linux-armv7l-cpython-312/MDAnalysis/coordinates/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates copying build/lib.linux-armv7l-cpython-312/MDAnalysis/coordinates/LAMMPS.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates copying build/lib.linux-armv7l-cpython-312/MDAnalysis/coordinates/timestep.pxd -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates copying build/lib.linux-armv7l-cpython-312/MDAnalysis/coordinates/core.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates copying build/lib.linux-armv7l-cpython-312/MDAnalysis/coordinates/ParmEd.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates copying build/lib.linux-armv7l-cpython-312/MDAnalysis/coordinates/XTC.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates copying build/lib.linux-armv7l-cpython-312/MDAnalysis/coordinates/null.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates copying build/lib.linux-armv7l-cpython-312/MDAnalysis/coordinates/chain.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates copying build/lib.linux-armv7l-cpython-312/MDAnalysis/coordinates/TXYZ.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates copying build/lib.linux-armv7l-cpython-312/MDAnalysis/coordinates/NAMDBIN.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates copying build/lib.linux-armv7l-cpython-312/MDAnalysis/coordinates/XYZ.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates copying build/lib.linux-armv7l-cpython-312/MDAnalysis/coordinates/FHIAIMS.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates copying build/lib.linux-armv7l-cpython-312/MDAnalysis/coordinates/GMS.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates copying build/lib.linux-armv7l-cpython-312/MDAnalysis/coordinates/timestep.cpython-312-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates copying build/lib.linux-armv7l-cpython-312/MDAnalysis/coordinates/PQR.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates copying build/lib.linux-armv7l-cpython-312/MDAnalysis/coordinates/TRZ.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates copying build/lib.linux-armv7l-cpython-312/MDAnalysis/coordinates/H5MD.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates copying build/lib.linux-armv7l-cpython-312/MDAnalysis/coordinates/PDBQT.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates copying build/lib.linux-armv7l-cpython-312/MDAnalysis/coordinates/MOL2.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates copying build/lib.linux-armv7l-cpython-312/MDAnalysis/coordinates/timestep.pyx -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates copying build/lib.linux-armv7l-cpython-312/MDAnalysis/coordinates/timestep.cpp -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates copying build/lib.linux-armv7l-cpython-312/MDAnalysis/coordinates/DCD.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates copying build/lib.linux-armv7l-cpython-312/MDAnalysis/coordinates/TRR.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates copying build/lib.linux-armv7l-cpython-312/MDAnalysis/coordinates/base.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates copying build/lib.linux-armv7l-cpython-312/MDAnalysis/coordinates/INPCRD.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates creating build/bdist.linux-armv7l/wheel/MDAnalysis/transformations copying build/lib.linux-armv7l-cpython-312/MDAnalysis/transformations/positionaveraging.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/transformations copying build/lib.linux-armv7l-cpython-312/MDAnalysis/transformations/wrap.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/transformations copying build/lib.linux-armv7l-cpython-312/MDAnalysis/transformations/rotate.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/transformations copying build/lib.linux-armv7l-cpython-312/MDAnalysis/transformations/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/transformations copying build/lib.linux-armv7l-cpython-312/MDAnalysis/transformations/fit.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/transformations copying build/lib.linux-armv7l-cpython-312/MDAnalysis/transformations/translate.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/transformations copying build/lib.linux-armv7l-cpython-312/MDAnalysis/transformations/nojump.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/transformations copying build/lib.linux-armv7l-cpython-312/MDAnalysis/transformations/boxdimensions.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/transformations copying build/lib.linux-armv7l-cpython-312/MDAnalysis/transformations/base.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/transformations creating build/bdist.linux-armv7l/wheel/MDAnalysis/lib copying build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/nsgrid.cpp -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib copying build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/_augment.cpython-312-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib copying build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/_augment.cpp -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib copying build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/log.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib copying build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/correlations.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib copying build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/NeighborSearch.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib copying build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/_cutil.pxd -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib copying build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/c_distances.cpython-312-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib copying build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/qcprot.cpython-312-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib copying build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/_transformations.cpython-312-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib creating build/bdist.linux-armv7l/wheel/MDAnalysis/lib/include copying build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/include/calc_distances.h -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/include copying build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/_cutil.cpython-312-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib copying build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/distances.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib copying build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/mdamath.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib copying build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/picklable_file_io.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib copying build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/c_distances_openmp.c -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib copying build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib copying build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/nsgrid.pyx -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib copying build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/c_distances_openmp.cpython-312-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib creating build/bdist.linux-armv7l/wheel/MDAnalysis/lib/src creating build/bdist.linux-armv7l/wheel/MDAnalysis/lib/src/transformations copying build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/src/transformations/AUTHOR -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/src/transformations copying build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/src/transformations/LICENCE -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/src/transformations copying build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/src/transformations/transformations.c -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/src/transformations creating build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats copying build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/formats/libmdaxdr.cpython-312-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats copying build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/formats/libdcd.pxd -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats copying build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/formats/cython_util.pxd -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats copying build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/formats/libmdaxdr.pyx -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats copying build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/formats/cython_util.cpython-312-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats creating build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats/include copying build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/formats/include/xdrfile.h -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats/include copying build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/formats/include/xdrfile_xtc.h -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats/include copying build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/formats/include/readdcd.h -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats/include copying build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/formats/include/trr_seek.h -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats/include copying build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/formats/include/fastio.h -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats/include copying build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/formats/include/endianswap.h -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats/include copying build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/formats/include/xtc_seek.h -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats/include copying build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/formats/include/xdrfile_trr.h -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats/include copying build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/formats/cython_util.c -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats copying build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/formats/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats copying build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/formats/libdcd.cpython-312-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats creating build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats/src copying build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/formats/src/xdrfile_xtc.c -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats/src copying build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/formats/src/xdrfile_trr.c -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats/src copying build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/formats/src/trr_seek.c -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats/src copying build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/formats/src/xtc_seek.c -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats/src copying build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/formats/src/xdrfile.c -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats/src copying build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/formats/libdcd.c -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats copying build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/formats/libmdaxdr.c -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats copying build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/formats/libmdaxdr.pxd -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats copying build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/formats/libdcd.pyx -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats copying build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/formats/cython_util.pyx -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats copying build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/_augment.pyx -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib copying build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/c_distances.c -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib copying build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/c_distances.pyx -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib copying build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/c_distances_openmp.pyx -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib copying build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/qcprot.pyx -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib copying build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/_distopia.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib copying build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/nsgrid.cpython-312-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib copying build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/_cutil.pyx -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib copying build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/pkdtree.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib copying build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/c_distances.pxd -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib copying build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/_cutil.cpp -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib copying build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/util.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib copying build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/qcprot.c -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib copying build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/transformations.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib creating build/bdist.linux-armv7l/wheel/MDAnalysis/lib/libmdanalysis copying build/lib.linux-armv7l-cpython-312/MDAnalysis/lib/libmdanalysis/__init__.pxd -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/libmdanalysis copying build/lib.linux-armv7l-cpython-312/MDAnalysis/authors.py -> build/bdist.linux-armv7l/wheel/MDAnalysis creating build/bdist.linux-armv7l/wheel/MDAnalysis/auxiliary copying build/lib.linux-armv7l-cpython-312/MDAnalysis/auxiliary/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/auxiliary copying build/lib.linux-armv7l-cpython-312/MDAnalysis/auxiliary/core.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/auxiliary copying build/lib.linux-armv7l-cpython-312/MDAnalysis/auxiliary/XVG.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/auxiliary copying build/lib.linux-armv7l-cpython-312/MDAnalysis/auxiliary/EDR.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/auxiliary copying build/lib.linux-armv7l-cpython-312/MDAnalysis/auxiliary/base.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/auxiliary creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis copying build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/nucleicacids.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis copying build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/nuclinfo.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis copying build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/align.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis copying build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/rdf.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis copying build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/msd.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis copying build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/density.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis copying build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/distances.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/legacy copying build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/legacy/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/legacy copying build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/legacy/x3dna.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/legacy copying build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/dihedrals.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis copying build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis copying build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/helix_analysis.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis copying build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/pca.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hydrogenbonds copying build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hydrogenbonds copying build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/hydrogenbonds/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hydrogenbonds copying build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/hydrogenbonds/hbond_autocorrel.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hydrogenbonds copying build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hydrogenbonds copying build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/psa.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis copying build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/polymer.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis copying build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/gnm.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis copying build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/waterdynamics.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis copying build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/atomicdistances.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis copying build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/bat.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hole2 copying build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/hole2/utils.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hole2 copying build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/hole2/hole.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hole2 copying build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/hole2/templates.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hole2 copying build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/hole2/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hole2 copying build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/lineardensity.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis copying build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/dielectric.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hbonds copying build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/hbonds/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hbonds copying build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/hbonds/hbond_autocorrel.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hbonds creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/data copying build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/data/rama_ref_data.npy -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/data copying build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/data/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/data copying build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/data/filenames.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/data copying build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/data/janin_ref_data.npy -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/data copying build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/contacts.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis copying build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/leaflet.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis copying build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/diffusionmap.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis copying build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/rms.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis copying build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/base.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore copying build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/encore/utils.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/dimensionality_reduction copying build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/dimensionality_reduction copying build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/dimensionality_reduction creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/dimensionality_reduction/include copying build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction/include/spe.h -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/dimensionality_reduction/include copying build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/dimensionality_reduction creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/dimensionality_reduction/src copying build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.c -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/dimensionality_reduction/src copying build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.cpython-312-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/dimensionality_reduction copying build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/dimensionality_reduction copying build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/dimensionality_reduction creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/clustering copying build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/encore/clustering/affinityprop.cpython-312-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/clustering creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/clustering/include copying build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/encore/clustering/include/ap.h -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/clustering/include copying build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/encore/clustering/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/clustering creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/clustering/src copying build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/encore/clustering/src/ap.c -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/clustering/src copying build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/encore/clustering/affinityprop.pyx -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/clustering copying build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/encore/clustering/affinityprop.c -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/clustering copying build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/encore/clustering/cluster.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/clustering copying build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/encore/clustering/ClusteringMethod.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/clustering copying build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/encore/clustering/ClusterCollection.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/clustering copying build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/encore/confdistmatrix.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore copying build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/encore/similarity.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore copying build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/encore/cutils.c -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore copying build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/encore/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore copying build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/encore/bootstrap.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore copying build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/encore/cutils.pyx -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore copying build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/encore/cutils.cpython-312-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore copying build/lib.linux-armv7l-cpython-312/MDAnalysis/analysis/encore/covariance.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore copying build/lib.linux-armv7l-cpython-312/MDAnalysis/units.py -> build/bdist.linux-armv7l/wheel/MDAnalysis copying build/lib.linux-armv7l-cpython-312/MDAnalysis/exceptions.py -> build/bdist.linux-armv7l/wheel/MDAnalysis running install_egg_info Copying MDAnalysis.egg-info to build/bdist.linux-armv7l/wheel/MDAnalysis-2.7.0.egg-info running install_scripts creating build/bdist.linux-armv7l/wheel/MDAnalysis-2.7.0.dist-info/WHEEL creating '/build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/.tmp-shqyv5id/MDAnalysis-2.7.0-cp312-cp312-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it adding 'MDAnalysis/__init__.py' adding 'MDAnalysis/authors.py' adding 'MDAnalysis/due.py' adding 'MDAnalysis/exceptions.py' adding 'MDAnalysis/units.py' adding 'MDAnalysis/version.py' adding 'MDAnalysis/analysis/__init__.py' adding 'MDAnalysis/analysis/align.py' adding 'MDAnalysis/analysis/atomicdistances.py' adding 'MDAnalysis/analysis/base.py' adding 'MDAnalysis/analysis/bat.py' adding 'MDAnalysis/analysis/contacts.py' adding 'MDAnalysis/analysis/density.py' adding 'MDAnalysis/analysis/dielectric.py' adding 'MDAnalysis/analysis/diffusionmap.py' adding 'MDAnalysis/analysis/dihedrals.py' adding 'MDAnalysis/analysis/distances.py' adding 'MDAnalysis/analysis/gnm.py' adding 'MDAnalysis/analysis/helix_analysis.py' adding 'MDAnalysis/analysis/leaflet.py' adding 'MDAnalysis/analysis/lineardensity.py' adding 'MDAnalysis/analysis/msd.py' adding 'MDAnalysis/analysis/nucleicacids.py' adding 'MDAnalysis/analysis/nuclinfo.py' adding 'MDAnalysis/analysis/pca.py' adding 'MDAnalysis/analysis/polymer.py' adding 'MDAnalysis/analysis/psa.py' adding 'MDAnalysis/analysis/rdf.py' adding 'MDAnalysis/analysis/rms.py' adding 'MDAnalysis/analysis/waterdynamics.py' adding 'MDAnalysis/analysis/data/__init__.py' adding 'MDAnalysis/analysis/data/filenames.py' adding 'MDAnalysis/analysis/data/janin_ref_data.npy' adding 'MDAnalysis/analysis/data/rama_ref_data.npy' adding 'MDAnalysis/analysis/encore/__init__.py' adding 'MDAnalysis/analysis/encore/bootstrap.py' adding 'MDAnalysis/analysis/encore/confdistmatrix.py' adding 'MDAnalysis/analysis/encore/covariance.py' adding 'MDAnalysis/analysis/encore/cutils.c' adding 'MDAnalysis/analysis/encore/cutils.cpython-312-arm-linux-gnueabihf.so' adding 'MDAnalysis/analysis/encore/cutils.pyx' adding 'MDAnalysis/analysis/encore/similarity.py' adding 'MDAnalysis/analysis/encore/utils.py' adding 'MDAnalysis/analysis/encore/clustering/ClusterCollection.py' adding 'MDAnalysis/analysis/encore/clustering/ClusteringMethod.py' adding 'MDAnalysis/analysis/encore/clustering/__init__.py' adding 'MDAnalysis/analysis/encore/clustering/affinityprop.c' adding 'MDAnalysis/analysis/encore/clustering/affinityprop.cpython-312-arm-linux-gnueabihf.so' adding 'MDAnalysis/analysis/encore/clustering/affinityprop.pyx' adding 'MDAnalysis/analysis/encore/clustering/cluster.py' adding 'MDAnalysis/analysis/encore/clustering/include/ap.h' adding 'MDAnalysis/analysis/encore/clustering/src/ap.c' adding 'MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py' adding 'MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py' adding 'MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py' adding 'MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c' adding 'MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.cpython-312-arm-linux-gnueabihf.so' adding 'MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx' adding 'MDAnalysis/analysis/encore/dimensionality_reduction/include/spe.h' adding 'MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.c' adding 'MDAnalysis/analysis/hbonds/__init__.py' adding 'MDAnalysis/analysis/hbonds/hbond_autocorrel.py' adding 'MDAnalysis/analysis/hole2/__init__.py' adding 'MDAnalysis/analysis/hole2/hole.py' adding 'MDAnalysis/analysis/hole2/templates.py' adding 'MDAnalysis/analysis/hole2/utils.py' adding 'MDAnalysis/analysis/hydrogenbonds/__init__.py' adding 'MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py' adding 'MDAnalysis/analysis/hydrogenbonds/hbond_autocorrel.py' adding 'MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py' adding 'MDAnalysis/analysis/legacy/__init__.py' adding 'MDAnalysis/analysis/legacy/x3dna.py' adding 'MDAnalysis/auxiliary/EDR.py' adding 'MDAnalysis/auxiliary/XVG.py' adding 'MDAnalysis/auxiliary/__init__.py' adding 'MDAnalysis/auxiliary/base.py' adding 'MDAnalysis/auxiliary/core.py' adding 'MDAnalysis/converters/OpenMM.py' adding 'MDAnalysis/converters/OpenMMParser.py' adding 'MDAnalysis/converters/ParmEd.py' adding 'MDAnalysis/converters/ParmEdParser.py' adding 'MDAnalysis/converters/RDKit.py' adding 'MDAnalysis/converters/RDKitParser.py' adding 'MDAnalysis/converters/__init__.py' adding 'MDAnalysis/converters/base.py' adding 'MDAnalysis/coordinates/CRD.py' adding 'MDAnalysis/coordinates/DCD.py' adding 'MDAnalysis/coordinates/DLPoly.py' adding 'MDAnalysis/coordinates/DMS.py' adding 'MDAnalysis/coordinates/FHIAIMS.py' adding 'MDAnalysis/coordinates/GMS.py' adding 'MDAnalysis/coordinates/GRO.py' adding 'MDAnalysis/coordinates/GSD.py' adding 'MDAnalysis/coordinates/H5MD.py' adding 'MDAnalysis/coordinates/INPCRD.py' adding 'MDAnalysis/coordinates/LAMMPS.py' adding 'MDAnalysis/coordinates/MMTF.py' adding 'MDAnalysis/coordinates/MOL2.py' adding 'MDAnalysis/coordinates/NAMDBIN.py' adding 'MDAnalysis/coordinates/PDB.py' adding 'MDAnalysis/coordinates/PDBQT.py' adding 'MDAnalysis/coordinates/PQR.py' adding 'MDAnalysis/coordinates/ParmEd.py' adding 'MDAnalysis/coordinates/TNG.py' adding 'MDAnalysis/coordinates/TRC.py' adding 'MDAnalysis/coordinates/TRJ.py' adding 'MDAnalysis/coordinates/TRR.py' adding 'MDAnalysis/coordinates/TRZ.py' adding 'MDAnalysis/coordinates/TXYZ.py' adding 'MDAnalysis/coordinates/XDR.py' adding 'MDAnalysis/coordinates/XTC.py' adding 'MDAnalysis/coordinates/XYZ.py' adding 'MDAnalysis/coordinates/__init__.py' adding 'MDAnalysis/coordinates/base.py' adding 'MDAnalysis/coordinates/chain.py' adding 'MDAnalysis/coordinates/chemfiles.py' adding 'MDAnalysis/coordinates/core.py' adding 'MDAnalysis/coordinates/memory.py' adding 'MDAnalysis/coordinates/null.py' adding 'MDAnalysis/coordinates/timestep.cpp' adding 'MDAnalysis/coordinates/timestep.cpython-312-arm-linux-gnueabihf.so' adding 'MDAnalysis/coordinates/timestep.pxd' adding 'MDAnalysis/coordinates/timestep.pyx' adding 'MDAnalysis/core/__init__.py' adding 'MDAnalysis/core/_get_readers.py' adding 'MDAnalysis/core/accessors.py' adding 'MDAnalysis/core/groups.py' adding 'MDAnalysis/core/selection.py' adding 'MDAnalysis/core/topology.py' adding 'MDAnalysis/core/topologyattrs.py' adding 'MDAnalysis/core/topologyobjects.py' adding 'MDAnalysis/core/universe.py' adding 'MDAnalysis/lib/NeighborSearch.py' adding 'MDAnalysis/lib/__init__.py' adding 'MDAnalysis/lib/_augment.cpp' adding 'MDAnalysis/lib/_augment.cpython-312-arm-linux-gnueabihf.so' adding 'MDAnalysis/lib/_augment.pyx' adding 'MDAnalysis/lib/_cutil.cpp' adding 'MDAnalysis/lib/_cutil.cpython-312-arm-linux-gnueabihf.so' adding 'MDAnalysis/lib/_cutil.pxd' adding 'MDAnalysis/lib/_cutil.pyx' adding 'MDAnalysis/lib/_distopia.py' adding 'MDAnalysis/lib/_transformations.cpython-312-arm-linux-gnueabihf.so' adding 'MDAnalysis/lib/c_distances.c' adding 'MDAnalysis/lib/c_distances.cpython-312-arm-linux-gnueabihf.so' adding 'MDAnalysis/lib/c_distances.pxd' adding 'MDAnalysis/lib/c_distances.pyx' adding 'MDAnalysis/lib/c_distances_openmp.c' adding 'MDAnalysis/lib/c_distances_openmp.cpython-312-arm-linux-gnueabihf.so' adding 'MDAnalysis/lib/c_distances_openmp.pyx' adding 'MDAnalysis/lib/correlations.py' adding 'MDAnalysis/lib/distances.py' adding 'MDAnalysis/lib/log.py' adding 'MDAnalysis/lib/mdamath.py' adding 'MDAnalysis/lib/nsgrid.cpp' adding 'MDAnalysis/lib/nsgrid.cpython-312-arm-linux-gnueabihf.so' adding 'MDAnalysis/lib/nsgrid.pyx' adding 'MDAnalysis/lib/picklable_file_io.py' adding 'MDAnalysis/lib/pkdtree.py' adding 'MDAnalysis/lib/qcprot.c' adding 'MDAnalysis/lib/qcprot.cpython-312-arm-linux-gnueabihf.so' adding 'MDAnalysis/lib/qcprot.pyx' adding 'MDAnalysis/lib/transformations.py' adding 'MDAnalysis/lib/util.py' adding 'MDAnalysis/lib/formats/__init__.py' adding 'MDAnalysis/lib/formats/cython_util.c' adding 'MDAnalysis/lib/formats/cython_util.cpython-312-arm-linux-gnueabihf.so' adding 'MDAnalysis/lib/formats/cython_util.pxd' adding 'MDAnalysis/lib/formats/cython_util.pyx' adding 'MDAnalysis/lib/formats/libdcd.c' adding 'MDAnalysis/lib/formats/libdcd.cpython-312-arm-linux-gnueabihf.so' adding 'MDAnalysis/lib/formats/libdcd.pxd' adding 'MDAnalysis/lib/formats/libdcd.pyx' adding 'MDAnalysis/lib/formats/libmdaxdr.c' adding 'MDAnalysis/lib/formats/libmdaxdr.cpython-312-arm-linux-gnueabihf.so' adding 'MDAnalysis/lib/formats/libmdaxdr.pxd' adding 'MDAnalysis/lib/formats/libmdaxdr.pyx' adding 'MDAnalysis/lib/formats/include/endianswap.h' adding 'MDAnalysis/lib/formats/include/fastio.h' adding 'MDAnalysis/lib/formats/include/readdcd.h' adding 'MDAnalysis/lib/formats/include/trr_seek.h' adding 'MDAnalysis/lib/formats/include/xdrfile.h' adding 'MDAnalysis/lib/formats/include/xdrfile_trr.h' adding 'MDAnalysis/lib/formats/include/xdrfile_xtc.h' adding 'MDAnalysis/lib/formats/include/xtc_seek.h' adding 'MDAnalysis/lib/formats/src/trr_seek.c' adding 'MDAnalysis/lib/formats/src/xdrfile.c' adding 'MDAnalysis/lib/formats/src/xdrfile_trr.c' adding 'MDAnalysis/lib/formats/src/xdrfile_xtc.c' adding 'MDAnalysis/lib/formats/src/xtc_seek.c' adding 'MDAnalysis/lib/include/calc_distances.h' adding 'MDAnalysis/lib/libmdanalysis/__init__.pxd' adding 'MDAnalysis/lib/src/transformations/AUTHOR' adding 'MDAnalysis/lib/src/transformations/LICENCE' adding 'MDAnalysis/lib/src/transformations/transformations.c' adding 'MDAnalysis/selections/__init__.py' adding 'MDAnalysis/selections/base.py' adding 'MDAnalysis/selections/charmm.py' adding 'MDAnalysis/selections/gromacs.py' adding 'MDAnalysis/selections/jmol.py' adding 'MDAnalysis/selections/pymol.py' adding 'MDAnalysis/selections/vmd.py' adding 'MDAnalysis/tests/__init__.py' adding 'MDAnalysis/tests/datafiles.py' adding 'MDAnalysis/topology/CRDParser.py' adding 'MDAnalysis/topology/DLPolyParser.py' adding 'MDAnalysis/topology/DMSParser.py' adding 'MDAnalysis/topology/ExtendedPDBParser.py' adding 'MDAnalysis/topology/FHIAIMSParser.py' adding 'MDAnalysis/topology/GMSParser.py' adding 'MDAnalysis/topology/GROParser.py' adding 'MDAnalysis/topology/GSDParser.py' adding 'MDAnalysis/topology/HoomdXMLParser.py' adding 'MDAnalysis/topology/ITPParser.py' adding 'MDAnalysis/topology/LAMMPSParser.py' adding 'MDAnalysis/topology/MMTFParser.py' adding 'MDAnalysis/topology/MOL2Parser.py' adding 'MDAnalysis/topology/MinimalParser.py' adding 'MDAnalysis/topology/PDBParser.py' adding 'MDAnalysis/topology/PDBQTParser.py' adding 'MDAnalysis/topology/PQRParser.py' adding 'MDAnalysis/topology/PSFParser.py' adding 'MDAnalysis/topology/ParmEdParser.py' adding 'MDAnalysis/topology/TOPParser.py' adding 'MDAnalysis/topology/TPRParser.py' adding 'MDAnalysis/topology/TXYZParser.py' adding 'MDAnalysis/topology/XYZParser.py' adding 'MDAnalysis/topology/__init__.py' adding 'MDAnalysis/topology/base.py' adding 'MDAnalysis/topology/core.py' adding 'MDAnalysis/topology/guessers.py' adding 'MDAnalysis/topology/tables.py' adding 'MDAnalysis/topology/tpr/__init__.py' adding 'MDAnalysis/topology/tpr/obj.py' adding 'MDAnalysis/topology/tpr/setting.py' adding 'MDAnalysis/topology/tpr/utils.py' adding 'MDAnalysis/transformations/__init__.py' adding 'MDAnalysis/transformations/base.py' adding 'MDAnalysis/transformations/boxdimensions.py' adding 'MDAnalysis/transformations/fit.py' adding 'MDAnalysis/transformations/nojump.py' adding 'MDAnalysis/transformations/positionaveraging.py' adding 'MDAnalysis/transformations/rotate.py' adding 'MDAnalysis/transformations/translate.py' adding 'MDAnalysis/transformations/wrap.py' adding 'MDAnalysis/visualization/__init__.py' adding 'MDAnalysis/visualization/streamlines.py' adding 'MDAnalysis/visualization/streamlines_3D.py' adding 'MDAnalysis-2.7.0.dist-info/AUTHORS' adding 'MDAnalysis-2.7.0.dist-info/LICENSE' adding 'MDAnalysis-2.7.0.dist-info/METADATA' adding 'MDAnalysis-2.7.0.dist-info/WHEEL' adding 'MDAnalysis-2.7.0.dist-info/top_level.txt' adding 'MDAnalysis-2.7.0.dist-info/RECORD' removing build/bdist.linux-armv7l/wheel Successfully built MDAnalysis-2.7.0-cp312-cp312-linux_armv7l.whl I: pybuild plugin_pyproject:144: Unpacking wheel built for python3.12 with "installer" module debian/rules execute_after_dh_auto_build-indep make[1]: Entering directory '/build/reproducible-path/mdanalysis-2.7.0' PYTHONPATH=/build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build make html -C package/doc/sphinx/ BUILDDIR=/build/reproducible-path/mdanalysis-2.7.0/.pybuild # HTML generator make[2]: Entering directory '/build/reproducible-path/mdanalysis-2.7.0/package/doc/sphinx' sphinx-build -v -b html source /build/reproducible-path/mdanalysis-2.7.0/.pybuild/html Running Sphinx v7.4.7 loading translations [en]... locale_dir /build/reproducible-path/mdanalysis-2.7.0/package/doc/sphinx/source/locales/en/LC_MESSAGES does not exist locale_dir /build/reproducible-path/mdanalysis-2.7.0/package/doc/sphinx/source/locales/en/LC_MESSAGES does not exist done making output directory... done Converting `source_suffix = '.rst'` to `source_suffix = {'.rst': 'restructuredtext'}`. checking bibtex cache... out of date parsing bibtex file /build/reproducible-path/mdanalysis-2.7.0/package/doc/sphinx/source/references.bib... parsed 66 entries locale_dir /build/reproducible-path/mdanalysis-2.7.0/package/doc/sphinx/source/locales/en/LC_MESSAGES does not exist loading intersphinx inventory 'h5py' from https://docs.h5py.org/en/stable/objects.inv... loading intersphinx inventory 'python' from https://docs.python.org/3/objects.inv... loading intersphinx inventory 'scipy' from https://docs.scipy.org/doc/scipy/objects.inv... WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://docs.h5py.org/en/stable/objects.inv' not fetchable due to : HTTPSConnectionPool(host='docs.h5py.org', port=443): Max retries exceeded with url: /en/stable/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) loading intersphinx inventory 'gsd' from https://gsd.readthedocs.io/en/stable/objects.inv... WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://docs.scipy.org/doc/scipy/objects.inv' not fetchable due to : HTTPSConnectionPool(host='docs.scipy.org', port=443): Max retries exceeded with url: /doc/scipy/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) loading intersphinx inventory 'maplotlib' from https://matplotlib.org/stable/objects.inv... loading intersphinx inventory 'griddataformats' from https://mdanalysis.org/GridDataFormats/objects.inv... WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://docs.python.org/3/objects.inv' not fetchable due to : HTTPSConnectionPool(host='docs.python.org', port=443): Max retries exceeded with url: /3/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://matplotlib.org/stable/objects.inv' not fetchable due to : HTTPSConnectionPool(host='matplotlib.org', port=443): Max retries exceeded with url: /stable/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://mdanalysis.org/GridDataFormats/objects.inv' not fetchable due to : HTTPSConnectionPool(host='mdanalysis.org', port=443): Max retries exceeded with url: /GridDataFormats/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://gsd.readthedocs.io/en/stable/objects.inv' not fetchable due to : HTTPSConnectionPool(host='gsd.readthedocs.io', port=443): Max retries exceeded with url: /en/stable/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) loading intersphinx inventory 'pmda' from https://mdanalysis.org/pmda/objects.inv... loading intersphinx inventory 'networkx' from https://networkx.org/documentation/stable/objects.inv... loading intersphinx inventory 'numpy' from https://numpy.org/doc/stable/objects.inv... loading intersphinx inventory 'parmed' from https://parmed.github.io/ParmEd/html/objects.inv... WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://networkx.org/documentation/stable/objects.inv' not fetchable due to : HTTPSConnectionPool(host='networkx.org', port=443): Max retries exceeded with url: /documentation/stable/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) loading intersphinx inventory 'rdkit' from https://rdkit.org/docs/objects.inv... WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://numpy.org/doc/stable/objects.inv' not fetchable due to : HTTPSConnectionPool(host='numpy.org', port=443): Max retries exceeded with url: /doc/stable/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://mdanalysis.org/pmda/objects.inv' not fetchable due to : HTTPSConnectionPool(host='mdanalysis.org', port=443): Max retries exceeded with url: /pmda/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://parmed.github.io/ParmEd/html/objects.inv' not fetchable due to : HTTPSConnectionPool(host='parmed.github.io', port=443): Max retries exceeded with url: /ParmEd/html/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://rdkit.org/docs/objects.inv' not fetchable due to : HTTPSConnectionPool(host='rdkit.org', port=443): Max retries exceeded with url: /docs/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) locale_dir /build/reproducible-path/mdanalysis-2.7.0/package/doc/sphinx/source/locales/en/LC_MESSAGES does not exist building [mo]: targets for 0 po files that are out of date writing output... building [html]: targets for 168 source files that are out of date updating environment: locale_dir /build/reproducible-path/mdanalysis-2.7.0/package/doc/sphinx/source/locales/en/LC_MESSAGES does not exist [new config] 168 added, 0 changed, 0 removed reading sources... [ 1%] documentation_pages/analysis/align /usr/lib/python3/dist-packages/Bio/Application/__init__.py:40: BiopythonDeprecationWarning: The Bio.Application modules and modules relying on it have been deprecated. Due to the on going maintenance burden of keeping command line application wrappers up to date, we have decided to deprecate and eventually remove these modules. We instead now recommend building your command line and invoking it directly with the subprocess module. warnings.warn( Didn't find AlignTraj.reference_atoms in MDAnalysis.analysis.align Didn't find AlignTraj.mobile_atoms in MDAnalysis.analysis.align Didn't find AlignTraj.results.rmsd in MDAnalysis.analysis.align Didn't find AlignTraj.filename in MDAnalysis.analysis.align Didn't find AverageStructure.reference_atoms in MDAnalysis.analysis.align Didn't find AverageStructure.mobile_atoms in MDAnalysis.analysis.align Didn't find AverageStructure.results.universe in MDAnalysis.analysis.align Didn't find AverageStructure.results.positions in MDAnalysis.analysis.align Didn't find AverageStructure.results.rmsd in MDAnalysis.analysis.align Didn't find AverageStructure.filename in MDAnalysis.analysis.align reading sources... [ 1%] documentation_pages/analysis/atomicdistances Didn't find AtomicDistances.results in MDAnalysis.analysis.atomicdistances Didn't find AtomicDistances.n_frames in MDAnalysis.analysis.atomicdistances Didn't find AtomicDistances.n_atoms in MDAnalysis.analysis.atomicdistances reading sources... [ 2%] documentation_pages/analysis/base Didn't find AnalysisBase.times in MDAnalysis.analysis.base Didn't find AnalysisBase.frames in MDAnalysis.analysis.base Didn't find AnalysisBase.results in MDAnalysis.analysis.base Didn't find AnalysisFromFunction.results.frames in MDAnalysis.analysis.base Didn't find AnalysisFromFunction.results.times in MDAnalysis.analysis.base Didn't find AnalysisFromFunction.results.timeseries in MDAnalysis.analysis.base Didn't find results.frames in MDAnalysis.analysis.base Didn't find results.times in MDAnalysis.analysis.base Didn't find results.timeseries in MDAnalysis.analysis.base reading sources... [ 2%] documentation_pages/analysis/bat Didn't find BAT.results.bat in MDAnalysis.analysis.bat reading sources... [ 3%] documentation_pages/analysis/contacts Didn't find Contacts.results.timeseries in MDAnalysis.analysis.contacts reading sources... [ 4%] documentation_pages/analysis/data reading sources... [ 4%] documentation_pages/analysis/density Didn't find DensityAnalysis.results.density in MDAnalysis.analysis.density Didn't find Density.grid in MDAnalysis.analysis.density Didn't find Density.edges in MDAnalysis.analysis.density Didn't find Density.delta in MDAnalysis.analysis.density Didn't find Density.origin in MDAnalysis.analysis.density Didn't find Density.units in MDAnalysis.analysis.density reading sources... [ 5%] documentation_pages/analysis/dielectric Didn't find DielectricConstant.results.M in MDAnalysis.analysis.dielectric Didn't find DielectricConstant.results.M2 in MDAnalysis.analysis.dielectric Didn't find DielectricConstant.results.fluct in MDAnalysis.analysis.dielectric Didn't find DielectricConstant.results.eps in MDAnalysis.analysis.dielectric Didn't find DielectricConstant.results.eps_mean in MDAnalysis.analysis.dielectric reading sources... [ 5%] documentation_pages/analysis/diffusionmap Didn't find DiffusionMap.eigenvalues in MDAnalysis.analysis.diffusionmap Didn't find DistanceMatrix.atoms in MDAnalysis.analysis.diffusionmap Didn't find DistanceMatrix.results.dist_matrix in MDAnalysis.analysis.diffusionmap reading sources... [ 6%] documentation_pages/analysis/dihedrals Matplotlib created a temporary cache directory at /tmp/matplotlib-cqxe7e20 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Didn't find Dihedral.results.angles in MDAnalysis.analysis.dihedrals Didn't find Ramachandran.results.angles in MDAnalysis.analysis.dihedrals Didn't find Janin.results.angles in MDAnalysis.analysis.dihedrals reading sources... [ 7%] documentation_pages/analysis/distances reading sources... [ 7%] documentation_pages/analysis/encore reading sources... [ 8%] documentation_pages/analysis/encore/bootstrap reading sources... [ 8%] documentation_pages/analysis/encore/clustering Didn't find Cluster.id in MDAnalysis.analysis.encore.clustering.ClusterCollection Didn't find Cluster.metadata in MDAnalysis.analysis.encore.clustering.ClusterCollection Didn't find Cluster.size in MDAnalysis.analysis.encore.clustering.ClusterCollection Didn't find Cluster.centroid in MDAnalysis.analysis.encore.clustering.ClusterCollection Didn't find Cluster.elements in MDAnalysis.analysis.encore.clustering.ClusterCollection Didn't find ClusterCollection.clusters in MDAnalysis.analysis.encore.clustering.ClusterCollection reading sources... [ 9%] documentation_pages/analysis/encore/confdistmatrix reading sources... [ 10%] documentation_pages/analysis/encore/covariance reading sources... [ 10%] documentation_pages/analysis/encore/dimensionality_reduction reading sources... [ 11%] documentation_pages/analysis/encore/similarity reading sources... [ 11%] documentation_pages/analysis/encore/utils Didn't find ParallelCalculation.n_jobs in MDAnalysis.analysis.encore.utils Didn't find ParallelCalculation.function in MDAnalysis.analysis.encore.utils Didn't find ParallelCalculation.args in MDAnalysis.analysis.encore.utils Didn't find ParallelCalculation.kwargs in MDAnalysis.analysis.encore.utils Didn't find ParallelCalculation.nruns in MDAnalysis.analysis.encore.utils reading sources... [ 12%] documentation_pages/analysis/gnm Didn't find GNMAnalysis.results.times in MDAnalysis.analysis.gnm Didn't find GNMAnalysis.results.eigenvalues in MDAnalysis.analysis.gnm Didn't find GNMAnalysis.results.eigenvectors in MDAnalysis.analysis.gnm Didn't find closeContactGNMAnalysis.results.times in MDAnalysis.analysis.gnm Didn't find closeContactGNMAnalysis.results.eigenvalues in MDAnalysis.analysis.gnm Didn't find closeContactGNMAnalysis.results.eigenvectors in MDAnalysis.analysis.gnm reading sources... [ 12%] documentation_pages/analysis/hbond_autocorrel reading sources... [ 13%] documentation_pages/analysis/hbond_autocorrel_deprecated /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/analysis/hbonds/hbond_autocorrel.py:52: DeprecationWarning: This module was moved to MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel; hbonds.hbond_autocorrel will be removed in 3.0.0. warnings.warn(wmsg, category=DeprecationWarning) reading sources... [ 14%] documentation_pages/analysis/helix_analysis Didn't find HELANAL.results.local_twists in MDAnalysis.analysis.helix_analysis Didn't find HELANAL.results.local_nres_per_turn in MDAnalysis.analysis.helix_analysis Didn't find HELANAL.results.local_axes in MDAnalysis.analysis.helix_analysis Didn't find HELANAL.results.local_heights in MDAnalysis.analysis.helix_analysis Didn't find HELANAL.results.local_helix_directions in MDAnalysis.analysis.helix_analysis Didn't find HELANAL.results.local_origins in MDAnalysis.analysis.helix_analysis Didn't find HELANAL.results.local_screw_angles in MDAnalysis.analysis.helix_analysis Didn't find HELANAL.results.local_bends in MDAnalysis.analysis.helix_analysis Didn't find HELANAL.results.all_bends in MDAnalysis.analysis.helix_analysis Didn't find HELANAL.results.global_axis in MDAnalysis.analysis.helix_analysis Didn't find HELANAL.results.global_tilts in MDAnalysis.analysis.helix_analysis Didn't find HELANAL.results.summary in MDAnalysis.analysis.helix_analysis reading sources... [ 14%] documentation_pages/analysis/hole2 Didn't find HoleAnalysis.results.sphpdbs in MDAnalysis.analysis.hole2 Didn't find HoleAnalysis.results.outfiles in MDAnalysis.analysis.hole2 Didn't find HoleAnalysis.results.profiles in MDAnalysis.analysis.hole2 reading sources... [ 15%] documentation_pages/analysis/hydrogenbonds Didn't find HydrogenBondAnalysis.results.hbonds in MDAnalysis.analysis.hydrogenbonds.hbond_analysis reading sources... [ 15%] documentation_pages/analysis/leaflet reading sources... [ 16%] documentation_pages/analysis/legacy/x3dna Didn't find X3DNA.profiles in MDAnalysis.analysis.legacy.x3dna Didn't find X3DNAtraj.profiles in MDAnalysis.analysis.legacy.x3dna reading sources... [ 17%] documentation_pages/analysis/legacy_modules reading sources... [ 17%] documentation_pages/analysis/lineardensity Didn't find LinearDensity.results.x.dim in MDAnalysis.analysis.lineardensity Didn't find LinearDensity.results.x.mass_density in MDAnalysis.analysis.lineardensity Didn't find LinearDensity.results.x.mass_density_stddev in MDAnalysis.analysis.lineardensity Didn't find LinearDensity.results.x.charge_density in MDAnalysis.analysis.lineardensity Didn't find LinearDensity.results.x.charge_density_stddev in MDAnalysis.analysis.lineardensity Didn't find LinearDensity.results.x.pos in MDAnalysis.analysis.lineardensity Didn't find LinearDensity.results.x.pos_std in MDAnalysis.analysis.lineardensity Didn't find LinearDensity.results.x.char in MDAnalysis.analysis.lineardensity Didn't find LinearDensity.results.x.char_std in MDAnalysis.analysis.lineardensity Didn't find LinearDensity.results.x.slice_volume in MDAnalysis.analysis.lineardensity Didn't find LinearDensity.results.x.hist_bin_edges in MDAnalysis.analysis.lineardensity Didn't find LinearDensity.Note in MDAnalysis.analysis.lineardensity reading sources... [ 18%] documentation_pages/analysis/msd Didn't find EinsteinMSD.dim_fac in MDAnalysis.analysis.msd Didn't find EinsteinMSD.results.timeseries in MDAnalysis.analysis.msd Didn't find EinsteinMSD.results.msds_by_particle in MDAnalysis.analysis.msd Didn't find EinsteinMSD.ag in MDAnalysis.analysis.msd Didn't find EinsteinMSD.n_frames in MDAnalysis.analysis.msd Didn't find EinsteinMSD.n_particles in MDAnalysis.analysis.msd reading sources... [ 18%] documentation_pages/analysis/nucleicacids Didn't find NucPairDist.results.pair_distances in MDAnalysis.analysis.nucleicacids Didn't find NucPairDist.results.distances in MDAnalysis.analysis.nucleicacids Didn't find NucPairDist.times in MDAnalysis.analysis.nucleicacids Didn't find WatsonCrickDist.results.distances in MDAnalysis.analysis.nucleicacids Didn't find WatsonCrickDist.results.pair_distances in MDAnalysis.analysis.nucleicacids Didn't find WatsonCrickDist.times in MDAnalysis.analysis.nucleicacids Didn't find MinorPairDist.results.distances in MDAnalysis.analysis.nucleicacids Didn't find MinorPairDist.times in MDAnalysis.analysis.nucleicacids Didn't find MajorPairDist.results.distances in MDAnalysis.analysis.nucleicacids Didn't find MajorPairDist.times in MDAnalysis.analysis.nucleicacids reading sources... [ 19%] documentation_pages/analysis/nuclinfo reading sources... [ 20%] documentation_pages/analysis/pca Didn't find PCA.results.p_components in MDAnalysis.analysis.pca Didn't find PCA.results.variance in MDAnalysis.analysis.pca Didn't find PCA.results.cumulated_variance in MDAnalysis.analysis.pca reading sources... [ 20%] documentation_pages/analysis/polymer Didn't find PersistenceLength.results.bond_autocorrelation in MDAnalysis.analysis.polymer Didn't find PersistenceLength.results.lb in MDAnalysis.analysis.polymer Didn't find PersistenceLength.results.x in MDAnalysis.analysis.polymer Didn't find PersistenceLength.results.lp in MDAnalysis.analysis.polymer Didn't find PersistenceLength.results.fit in MDAnalysis.analysis.polymer reading sources... [ 21%] documentation_pages/analysis/psa Didn't find Path.u_original in MDAnalysis.analysis.psa Didn't find Path.u_reference in MDAnalysis.analysis.psa Didn't find Path.select in MDAnalysis.analysis.psa Didn't find Path.path_select in MDAnalysis.analysis.psa Didn't find Path.ref_frame in MDAnalysis.analysis.psa Didn't find Path.u_fitted in MDAnalysis.analysis.psa Didn't find Path.path in MDAnalysis.analysis.psa Didn't find PSAPair.npaths in MDAnalysis.analysis.psa Didn't find PSAPair.matrix_id in MDAnalysis.analysis.psa Didn't find PSAPair.pair_id in MDAnalysis.analysis.psa Didn't find PSAPair.nearest_neighbors in MDAnalysis.analysis.psa Didn't find PSAPair.hausdorff_pair in MDAnalysis.analysis.psa Didn't find PSAnalysis.universes in MDAnalysis.analysis.psa Didn't find PSAnalysis.u_reference in MDAnalysis.analysis.psa Didn't find PSAnalysis.select in MDAnalysis.analysis.psa Didn't find PSAnalysis.path_select in MDAnalysis.analysis.psa Didn't find PSAnalysis.ref_frame in MDAnalysis.analysis.psa Didn't find PSAnalysis.paths in MDAnalysis.analysis.psa Didn't find PSAnalysis.D in MDAnalysis.analysis.psa reading sources... [ 21%] documentation_pages/analysis/rdf Didn't find InterRDF.results.bins in MDAnalysis.analysis.rdf Didn't find InterRDF.results.edges in MDAnalysis.analysis.rdf Didn't find InterRDF.results.rdf in MDAnalysis.analysis.rdf Didn't find InterRDF.results.count in MDAnalysis.analysis.rdf Didn't find InterRDF_s.results.bins in MDAnalysis.analysis.rdf Didn't find InterRDF_s.results.edges in MDAnalysis.analysis.rdf Didn't find InterRDF_s.results.rdf in MDAnalysis.analysis.rdf Didn't find InterRDF_s.results.count in MDAnalysis.analysis.rdf Didn't find InterRDF_s.results.cdf in MDAnalysis.analysis.rdf reading sources... [ 22%] documentation_pages/analysis/rms Didn't find RMSD.results.rmsd in MDAnalysis.analysis.rms Didn't find RMSF.results.rmsf in MDAnalysis.analysis.rms reading sources... [ 23%] documentation_pages/analysis/waterdynamics reading sources... [ 23%] documentation_pages/analysis/wbridge_analysis Didn't find WaterBridgeAnalysis.timesteps in MDAnalysis.analysis.hydrogenbonds.wbridge_analysis Didn't find WaterBridgeAnalysis.results.network in MDAnalysis.analysis.hydrogenbonds.wbridge_analysis Didn't find WaterBridgeAnalysis.table in MDAnalysis.analysis.hydrogenbonds.wbridge_analysis Didn't find WaterBridgeAnalysis.results.timeseries in MDAnalysis.analysis.hydrogenbonds.wbridge_analysis reading sources... [ 24%] documentation_pages/analysis_modules reading sources... [ 24%] documentation_pages/auxiliary/EDR Didn't find EDRReader._auxdata in MDAnalysis.auxiliary.EDR Didn't find EDRReader.data_dict in MDAnalysis.auxiliary.EDR Didn't find EDRReader.unit_dict in MDAnalysis.auxiliary.EDR Didn't find EDRReader._n_steps in MDAnalysis.auxiliary.EDR Didn't find EDRReader.terms in MDAnalysis.auxiliary.EDR reading sources... [ 25%] documentation_pages/auxiliary/XVG reading sources... [ 26%] documentation_pages/auxiliary/base Didn't find AuxStep.step in MDAnalysis.auxiliary.base Didn't find AuxReader.auxstep in MDAnalysis.auxiliary.base Didn't find AuxReader.frame_data in MDAnalysis.auxiliary.base Didn't find AuxReader.frame_rep in MDAnalysis.auxiliary.base Didn't find AuxFileReader.auxfile in MDAnalysis.auxiliary.base reading sources... [ 26%] documentation_pages/auxiliary/core reading sources... [ 27%] documentation_pages/auxiliary/init reading sources... [ 27%] documentation_pages/auxiliary_modules reading sources... [ 28%] documentation_pages/converters reading sources... [ 29%] documentation_pages/converters/OpenMM reading sources... [ 29%] documentation_pages/converters/ParmEd reading sources... [ 30%] documentation_pages/converters/RDKit reading sources... [ 30%] documentation_pages/converters/base reading sources... [ 31%] documentation_pages/coordinates/CRD reading sources... [ 32%] documentation_pages/coordinates/DCD reading sources... [ 32%] documentation_pages/coordinates/DLPoly reading sources... [ 33%] documentation_pages/coordinates/DMS reading sources... [ 33%] documentation_pages/coordinates/FHIAIMS reading sources... [ 34%] documentation_pages/coordinates/GMS reading sources... [ 35%] documentation_pages/coordinates/GRO reading sources... [ 35%] documentation_pages/coordinates/GSD reading sources... [ 36%] documentation_pages/coordinates/H5MD reading sources... [ 36%] documentation_pages/coordinates/INPCRD reading sources... [ 37%] documentation_pages/coordinates/LAMMPS reading sources... [ 38%] documentation_pages/coordinates/MMTF reading sources... [ 38%] documentation_pages/coordinates/MOL2 reading sources... [ 39%] documentation_pages/coordinates/NAMDBIN reading sources... [ 39%] documentation_pages/coordinates/PDB reading sources... [ 40%] documentation_pages/coordinates/PDBQT reading sources... [ 40%] documentation_pages/coordinates/PQR reading sources... [ 41%] documentation_pages/coordinates/TNG reading sources... [ 42%] documentation_pages/coordinates/TRC reading sources... [ 42%] documentation_pages/coordinates/TRJ reading sources... [ 43%] documentation_pages/coordinates/TRR reading sources... [ 43%] documentation_pages/coordinates/TRZ Didn't find TRZReader.ts in MDAnalysis.coordinates.TRZ reading sources... [ 44%] documentation_pages/coordinates/TXYZ reading sources... [ 45%] documentation_pages/coordinates/XDR reading sources... [ 45%] documentation_pages/coordinates/XTC reading sources... [ 46%] documentation_pages/coordinates/XYZ reading sources... [ 46%] documentation_pages/coordinates/base reading sources... [ 47%] documentation_pages/coordinates/chain reading sources... [ 48%] documentation_pages/coordinates/chemfiles reading sources... [ 48%] documentation_pages/coordinates/core reading sources... [ 49%] documentation_pages/coordinates/init reading sources... [ 49%] documentation_pages/coordinates/memory reading sources... [ 50%] documentation_pages/coordinates/null reading sources... [ 51%] documentation_pages/coordinates/pickle_readers reading sources... [ 51%] documentation_pages/coordinates/timestep reading sources... [ 52%] documentation_pages/coordinates_modules reading sources... [ 52%] documentation_pages/core/accessors reading sources... [ 53%] documentation_pages/core/groups reading sources... [ 54%] documentation_pages/core/init reading sources... [ 54%] documentation_pages/core/selection reading sources... [ 55%] documentation_pages/core/topology Didn't find TransTable.n_atoms in MDAnalysis.core.topology Didn't find TransTable.n_residues in MDAnalysis.core.topology Didn't find TransTable.n_segments in MDAnalysis.core.topology reading sources... [ 55%] documentation_pages/core/topologyattrs reading sources... [ 56%] documentation_pages/core/topologyobjects reading sources... [ 57%] documentation_pages/core/universe Didn't find Universe.atoms in MDAnalysis.core.universe Didn't find Universe.residues in MDAnalysis.core.universe Didn't find Universe.segments in MDAnalysis.core.universe reading sources... [ 57%] documentation_pages/core_modules reading sources... [ 58%] documentation_pages/exceptions reading sources... [ 58%] documentation_pages/lib/NeighborSearch reading sources... [ 59%] documentation_pages/lib/c_distances reading sources... [ 60%] documentation_pages/lib/c_distances_openmp reading sources... [ 60%] documentation_pages/lib/correlations reading sources... [ 61%] documentation_pages/lib/distances reading sources... [ 61%] documentation_pages/lib/formats/libdcd reading sources... [ 62%] documentation_pages/lib/formats/libmdaxdr reading sources... [ 62%] documentation_pages/lib/log reading sources... [ 63%] documentation_pages/lib/mdamath reading sources... [ 64%] documentation_pages/lib/nsgrid reading sources... [ 64%] documentation_pages/lib/picklable_file_io reading sources... [ 65%] documentation_pages/lib/pkdtree reading sources... [ 65%] documentation_pages/lib/qcprot reading sources... [ 66%] documentation_pages/lib/transformations reading sources... [ 67%] documentation_pages/lib/util reading sources... [ 67%] documentation_pages/lib_modules reading sources... [ 68%] documentation_pages/overview reading sources... [ 68%] documentation_pages/references reading sources... [ 69%] documentation_pages/selections reading sources... [ 70%] documentation_pages/selections/base reading sources... [ 70%] documentation_pages/selections/charmm reading sources... [ 71%] documentation_pages/selections/gromacs reading sources... [ 71%] documentation_pages/selections/jmol reading sources... [ 72%] documentation_pages/selections/pymol reading sources... [ 73%] documentation_pages/selections/vmd reading sources... [ 73%] documentation_pages/selections_modules reading sources... [ 74%] documentation_pages/topology reading sources... [ 74%] documentation_pages/topology/CRDParser reading sources... [ 75%] documentation_pages/topology/DLPolyParser reading sources... [ 76%] documentation_pages/topology/DMSParser reading sources... [ 76%] documentation_pages/topology/ExtendedPDBParser reading sources... [ 77%] documentation_pages/topology/FHIAIMSParser reading sources... [ 77%] documentation_pages/topology/GMSParser reading sources... [ 78%] documentation_pages/topology/GROParser reading sources... [ 79%] documentation_pages/topology/GSDParser reading sources... [ 79%] documentation_pages/topology/HoomdXMLParser reading sources... [ 80%] documentation_pages/topology/ITPParser reading sources... [ 80%] documentation_pages/topology/LAMMPSParser reading sources... [ 81%] documentation_pages/topology/MMTFParser reading sources... [ 82%] documentation_pages/topology/MOL2Parser reading sources... [ 82%] documentation_pages/topology/MinimalParser reading sources... [ 83%] documentation_pages/topology/PDBParser reading sources... [ 83%] documentation_pages/topology/PDBQTParser reading sources... [ 84%] documentation_pages/topology/PQRParser reading sources... [ 85%] documentation_pages/topology/PSFParser reading sources... [ 85%] documentation_pages/topology/TOPParser reading sources... [ 86%] documentation_pages/topology/TPRParser reading sources... [ 86%] documentation_pages/topology/TXYZParser reading sources... [ 87%] documentation_pages/topology/XYZParser reading sources... [ 88%] documentation_pages/topology/base reading sources... [ 88%] documentation_pages/topology/core reading sources... [ 89%] documentation_pages/topology/guessers reading sources... [ 89%] documentation_pages/topology/init reading sources... [ 90%] documentation_pages/topology/tables reading sources... [ 90%] documentation_pages/topology/tpr_util reading sources... [ 91%] documentation_pages/topology_modules reading sources... 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[100%] index /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/lib/util.py:docstring of MDAnalysis.lib.util.openany:3: WARNING: unknown keyword: 'with' /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/lib/util.py:docstring of MDAnalysis.lib.util.anyopen:25: WARNING: unknown keyword: 'with' /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/lib/util.py:docstring of MDAnalysis.lib.util.NamedStream:32: WARNING: unknown keyword: 'with' /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/lib/util.py:docstring of MDAnalysis.lib.util.NamedStream:67: WARNING: unknown keyword: 'with' /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/lib/util.py:docstring of MDAnalysis.lib.util.NamedStream:74: WARNING: unknown keyword: 'with' generating indices... genindex py-modindex done highlighting module code... 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[100%] =============================== warnings summary =============================== ../../../usr/lib/python3/dist-packages/Bio/Application/__init__.py:40 /usr/lib/python3/dist-packages/Bio/Application/__init__.py:40: BiopythonDeprecationWarning: The Bio.Application modules and modules relying on it have been deprecated. Due to the on going maintenance burden of keeping command line application wrappers up to date, we have decided to deprecate and eventually remove these modules. We instead now recommend building your command line and invoking it directly with the subprocess module. warnings.warn( .pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/DCD.py:165: 2 warnings MDAnalysisTests/analysis/test_align.py: 77 warnings MDAnalysisTests/analysis/test_base.py: 3 warnings MDAnalysisTests/analysis/test_bat.py: 2 warnings MDAnalysisTests/analysis/test_contacts.py: 21 warnings MDAnalysisTests/analysis/test_dielectric.py: 6 warnings MDAnalysisTests/analysis/test_encore.py: 10 warnings MDAnalysisTests/analysis/test_helix_analysis.py: 7 warnings MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py: 1 warning MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py: 1 warning MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py: 6 warnings MDAnalysisTests/analysis/test_lineardensity.py: 6 warnings MDAnalysisTests/analysis/test_msd.py: 2 warnings MDAnalysisTests/analysis/test_pca.py: 12 warnings MDAnalysisTests/analysis/test_psa.py: 124 warnings MDAnalysisTests/analysis/test_rms.py: 38 warnings MDAnalysisTests/analysis/test_waterdynamics.py: 1 warning MDAnalysisTests/coordinates/test_chainreader.py: 72 warnings MDAnalysisTests/coordinates/test_copying.py: 18 warnings MDAnalysisTests/coordinates/test_dcd.py: 112 warnings MDAnalysisTests/coordinates/test_lammps.py: 5 warnings MDAnalysisTests/coordinates/test_memory.py: 88 warnings MDAnalysisTests/coordinates/test_pdb.py: 7 warnings MDAnalysisTests/coordinates/test_timestep_api.py: 5 warnings MDAnalysisTests/core/test_accumulate.py: 48 warnings MDAnalysisTests/core/test_atom.py: 15 warnings MDAnalysisTests/core/test_atomgroup.py: 170 warnings MDAnalysisTests/core/test_atomselections.py: 4 warnings MDAnalysisTests/core/test_copying.py: 6 warnings MDAnalysisTests/core/test_groups.py: 11 warnings MDAnalysisTests/core/test_residue.py: 4 warnings MDAnalysisTests/core/test_residuegroup.py: 23 warnings MDAnalysisTests/core/test_segmentgroup.py: 9 warnings MDAnalysisTests/core/test_topologyattrs.py: 8 warnings MDAnalysisTests/core/test_topologyobjects.py: 4 warnings MDAnalysisTests/core/test_universe.py: 31 warnings MDAnalysisTests/lib/test_distances.py: 46 warnings MDAnalysisTests/lib/test_neighborsearch.py: 2 warnings MDAnalysisTests/lib/test_qcprot.py: 2 warnings MDAnalysisTests/lib/test_util.py: 67 warnings MDAnalysisTests/parallelism/test_multiprocessing.py: 3 warnings MDAnalysisTests/parallelism/test_pickle_transformation.py: 8 warnings MDAnalysisTests/topology/test_guessers.py: 1 warning MDAnalysisTests/topology/test_minimal.py: 2 warnings MDAnalysisTests/transformations/test_base.py: 1 warning MDAnalysisTests/transformations/test_nojump.py: 3 warnings MDAnalysisTests/utils/test_modelling.py: 3 warnings MDAnalysisTests/utils/test_selections.py: 20 warnings /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/DCD.py:165: DeprecationWarning: DCDReader currently makes independent timesteps by copying self.ts while other readers update self.ts inplace. This behavior will be changed in 3.0 to be the same as other readers. Read more at https://github.com/MDAnalysis/mdanalysis/issues/3889 to learn if this change in behavior might affect you. warnings.warn("DCDReader currently makes independent timesteps" .pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/analysis/hbonds/hbond_autocorrel.py:52 /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/analysis/hbonds/hbond_autocorrel.py:52: DeprecationWarning: This module was moved to MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel; hbonds.hbond_autocorrel will be removed in 3.0.0. warnings.warn(wmsg, category=DeprecationWarning) .pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/chemfiles.py:122 .pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/chemfiles.py:122 .pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/chemfiles.py:122 MDAnalysisTests/coordinates/test_writer_api.py::test_ts_error[ChemfilesWriter] MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[ChemfilesWriter] MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[ChemfilesWriter] /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/chemfiles.py:122: UserWarning: chemfiles package not found, try installing it with 'pip install chemfiles' warnings.warn( MDAnalysisTests/analysis/test_align.py: 699 warnings MDAnalysisTests/analysis/test_psa.py: 5960 warnings MDAnalysisTests/coordinates/test_chainreader.py: 298 warnings MDAnalysisTests/coordinates/test_dcd.py: 687 warnings MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings MDAnalysisTests/core/test_atomgroup.py: 318 warnings /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/DCD.py:463: UserWarning: No dimensions set for current frame, zeroed unitcell will be written warnings.warn(wmsg) MDAnalysisTests/analysis/test_align.py: 5 warnings MDAnalysisTests/analysis/test_encore.py: 203 warnings MDAnalysisTests/coordinates/test_memory.py: 9 warnings MDAnalysisTests/core/test_universe.py: 17 warnings /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/memory.py:535: DeprecationWarning: asel argument to timeseries will be renamed to'atomgroup' in 3.0, see #3911 warnings.warn( MDAnalysisTests/analysis/test_bat.py: 9 warnings MDAnalysisTests/coordinates/test_mol2.py: 3 warnings /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/topology/MOL2Parser.py:234: UserWarning: Unknown elements found for some atoms: {'ho', 'oh', 'hc', 'h1', 'c3'}. These have been given an empty element record. warnings.warn("Unknown elements found for some " MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_userdefn_neqbox MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_userdefn_boxshape MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_gridcenter_shape MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_gridcenter_type MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_gridcenter_missing MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_xdim_type MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_xdim_nanvalue /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/analysis/density.py:423: UserWarning: Box padding (currently set at 2.0) is not used in user defined grids. warnings.warn(msg) MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_userdefn_neqbox MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_userdefn_boxshape MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_warn_userdefn_padding /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/analysis/density.py:556: UserWarning: Atom selection does not fit grid --- you may want to define a larger box warnings.warn(msg) MDAnalysisTests/analysis/test_dihedrals.py::TestRamachandran::test_ramachandran MDAnalysisTests/analysis/test_dihedrals.py::TestRamachandran::test_ramachandran_single_frame MDAnalysisTests/analysis/test_dihedrals.py::TestRamachandran::test_ramachandran_residue_selections MDAnalysisTests/analysis/test_dihedrals.py::TestRamachandran::test_ramachandran_attr_warning /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/analysis/dihedrals.py:400: UserWarning: Cannot determine phi and psi angles for the first or last residues warnings.warn("Cannot determine phi and psi angles for the first " MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_janin MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_janin_tpr MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_janin_single_frame MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_plot MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_janin_attr_warning /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/analysis/dihedrals.py:582: UserWarning: All residues selected with 'resname ALA CYS* GLY PRO SER THR VAL' have been removed from the selection. warnings.warn(f"All residues selected with '{select_remove}' " MDAnalysisTests/analysis/test_encore.py: 5 warnings MDAnalysisTests/parallelism/test_multiprocessing.py: 34 warnings MDAnalysisTests/visualization/test_streamlines.py: 3 warnings /usr/lib/python3.12/multiprocessing/popen_fork.py:66: DeprecationWarning: This process (pid=11053) is multi-threaded, use of fork() may lead to deadlocks in the child. self.pid = os.fork() MDAnalysisTests/analysis/test_helix_analysis.py::test_local_screw_angles_plane_circle MDAnalysisTests/analysis/test_helix_analysis.py::test_local_screw_angles_ortho_circle MDAnalysisTests/analysis/test_helix_analysis.py::test_local_screw_angles_parallel_axes /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/analysis/helix_analysis.py:181: RuntimeWarning: invalid value encountered in divide cos = cos_perp, cos_ortho = np.matmul(refs, proj_plane.T)/norms MDAnalysisTests/analysis/test_helix_analysis.py: 30 warnings /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/analysis/helix_analysis.py:262: RuntimeWarning: invalid value encountered in divide local_axes = (cross_bi.T / mdamath.pnorm(cross_bi)).T # (n_res-3, 3) MDAnalysisTests/analysis/test_helix_analysis.py: 176 warnings /usr/lib/python3/dist-packages/numpy/core/_methods.py:206: RuntimeWarning: Degrees of freedom <= 0 for slice ret = _var(a, axis=axis, dtype=dtype, out=out, ddof=ddof, MDAnalysisTests/analysis/test_helix_analysis.py: 160 warnings /usr/lib/python3/dist-packages/numpy/core/_methods.py:195: RuntimeWarning: invalid value encountered in divide ret = um.true_divide( MDAnalysisTests/analysis/test_helix_analysis.py: 16 warnings /usr/lib/python3/dist-packages/numpy/core/_methods.py:198: RuntimeWarning: invalid value encountered in scalar divide ret = ret.dtype.type(ret / rcount) MDAnalysisTests/analysis/test_hole2.py: 1 warning MDAnalysisTests/coordinates/test_pdb.py: 16 warnings MDAnalysisTests/core/test_atomgroup.py: 26 warnings MDAnalysisTests/core/test_atomselections.py: 1 warning MDAnalysisTests/core/test_topologyattrs.py: 1 warning MDAnalysisTests/topology/test_pdb.py: 1 warning MDAnalysisTests/utils/test_modelling.py: 1 warning /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/PDB.py:453: UserWarning: 1 A^3 CRYST1 record, this is usually a placeholder. Unit cell dimensions will be set to None. warnings.warn("1 A^3 CRYST1 record," MDAnalysisTests/analysis/test_hole2.py: 1 warning MDAnalysisTests/coordinates/test_pdb.py: 23 warnings MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings MDAnalysisTests/core/test_atomgroup.py: 15 warnings MDAnalysisTests/utils/test_modelling.py: 1 warning /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/PDB.py:777: UserWarning: Unit cell dimensions not found. CRYST1 record set to unitary values. warnings.warn("Unit cell dimensions not found. " MDAnalysisTests/analysis/test_hole2.py: 1 warning MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings MDAnalysisTests/coordinates/test_pdb.py: 22 warnings MDAnalysisTests/coordinates/test_trz.py: 1 warning MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings MDAnalysisTests/core/test_atomgroup.py: 15 warnings MDAnalysisTests/transformations/test_nojump.py: 1 warning MDAnalysisTests/utils/test_modelling.py: 2 warnings /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'elements' Using default value of ' ' warnings.warn("Found no information for attr: '{}'" MDAnalysisTests/analysis/test_hole2.py: 1 warning MDAnalysisTests/coordinates/test_h5md.py: 3 warnings MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings MDAnalysisTests/coordinates/test_pdb.py: 32 warnings MDAnalysisTests/coordinates/test_trz.py: 1 warning MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings MDAnalysisTests/core/test_atomgroup.py: 15 warnings MDAnalysisTests/topology/test_altloc.py: 1 warning MDAnalysisTests/transformations/test_nojump.py: 1 warning MDAnalysisTests/utils/test_modelling.py: 3 warnings /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'formalcharges' Using default value of '0' warnings.warn("Found no information for attr: '{}'" MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py: 13 warnings MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py: 14 warnings MDAnalysisTests/analysis/test_persistencelength.py: 1 warning MDAnalysisTests/coordinates/test_copying.py: 18 warnings MDAnalysisTests/coordinates/test_timestep_api.py: 3 warnings MDAnalysisTests/coordinates/test_trz.py: 5 warnings MDAnalysisTests/core/test_atomgroup.py: 39 warnings MDAnalysisTests/core/test_atomselections.py: 14 warnings MDAnalysisTests/core/test_topologyobjects.py: 1 warning MDAnalysisTests/core/test_universe.py: 3 warnings MDAnalysisTests/core/test_wrap.py: 13 warnings MDAnalysisTests/parallelism/test_multiprocessing.py: 1 warning MDAnalysisTests/topology/test_minimal.py: 1 warning /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/TRZ.py:119: DeprecationWarning: The TRZ reader is deprecated and will be removed in MDAnalysis version 3.0.0 warnings.warn(wmsg, DeprecationWarning) MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py: 9 warnings MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py: 10 warnings /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/analysis/hydrogenbonds/hbond_autocorrel.py:377: RuntimeWarning: Desired number of sample points too high, using 6 warnings.warn("Desired number of sample points too high, using {0}" MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_continuous /build/reproducible-path/mdanalysis-2.7.0/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:62: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! `HydrogenBondAutoCorrel` will be removed in release 3.0.0. The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. hbond = HBAC(u, MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_continuous_excl /build/reproducible-path/mdanalysis-2.7.0/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:79: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! `HydrogenBondAutoCorrel` will be removed in release 3.0.0. The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. hbond = HBAC(u, MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_intermittent /build/reproducible-path/mdanalysis-2.7.0/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:99: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! `HydrogenBondAutoCorrel` will be removed in release 3.0.0. The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. hbond = HBAC(u, MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_intermittent_timecut /build/reproducible-path/mdanalysis-2.7.0/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:117: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! `HydrogenBondAutoCorrel` will be removed in release 3.0.0. The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. hbond = HBAC(u, MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_intermittent_excl /build/reproducible-path/mdanalysis-2.7.0/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:135: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! `HydrogenBondAutoCorrel` will be removed in release 3.0.0. The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. hbond = HBAC(u, MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_solve_continuous /build/reproducible-path/mdanalysis-2.7.0/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:156: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! `HydrogenBondAutoCorrel` will be removed in release 3.0.0. The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. hbond = HBAC(u, MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_solve_intermittent /build/reproducible-path/mdanalysis-2.7.0/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:181: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! `HydrogenBondAutoCorrel` will be removed in release 3.0.0. The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. hbond = HBAC(u, MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_wronglength_DA /build/reproducible-path/mdanalysis-2.7.0/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:210: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! `HydrogenBondAutoCorrel` will be removed in release 3.0.0. The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. HBAC(u, MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_exclusions /build/reproducible-path/mdanalysis-2.7.0/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:225: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! `HydrogenBondAutoCorrel` will be removed in release 3.0.0. The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. HBAC(u, MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_bond_type_VE /build/reproducible-path/mdanalysis-2.7.0/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:236: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! `HydrogenBondAutoCorrel` will be removed in release 3.0.0. The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. HBAC(u, MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_solve_before_run_VE /build/reproducible-path/mdanalysis-2.7.0/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:247: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! `HydrogenBondAutoCorrel` will be removed in release 3.0.0. The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. hbond = HBAC(u, MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_unslicable_traj_VE /build/reproducible-path/mdanalysis-2.7.0/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:262: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! `HydrogenBondAutoCorrel` will be removed in release 3.0.0. The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. HBAC( MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_repr /build/reproducible-path/mdanalysis-2.7.0/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:272: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! `HydrogenBondAutoCorrel` will be removed in release 3.0.0. The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. hbond = HBAC(u, MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::test_find_donors /build/reproducible-path/mdanalysis-2.7.0/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:300: DeprecationWarning: `find_hydrogen_donors` is deprecated! `find_hydrogen_donors` will be removed in release 3.0.0. The function was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. D = hbonds.find_hydrogen_donors(H) MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::test_donors_nobonds /build/reproducible-path/mdanalysis-2.7.0/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:312: DeprecationWarning: `find_hydrogen_donors` is deprecated! `find_hydrogen_donors` will be removed in release 3.0.0. The function was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. hbonds.find_hydrogen_donors(u.atoms) MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisIdeal::test_count_by_type /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py:733: UserWarning: No hydrogen bonds were found given d-a cutoff of 3.0 between Donor, name O, and Acceptor, name O. warnings.warn( MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisIdeal::test_count_by_type /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py:765: UserWarning: No hydrogen bonds were found given angle of 120.0 between Donor, name O, and Acceptor, name O. warnings.warn( MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisIdeal::test_logging_step_not_1 MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_logging_step_not_1 MDAnalysisTests/analysis/test_waterdynamics.py::test_SurvivalProbability_zeroMolecules MDAnalysisTests/analysis/test_waterdynamics.py::test_SurvivalProbability_zeroMolecules MDAnalysisTests/analysis/test_waterdynamics.py::test_SurvivalProbability_zeroMolecules /usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:3504: RuntimeWarning: Mean of empty slice. return _methods._mean(a, axis=axis, dtype=dtype, MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisIdeal::test_logging_step_not_1 MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_logging_step_not_1 MDAnalysisTests/analysis/test_waterdynamics.py::test_SurvivalProbability_zeroMolecules MDAnalysisTests/analysis/test_waterdynamics.py::test_SurvivalProbability_zeroMolecules MDAnalysisTests/analysis/test_waterdynamics.py::test_SurvivalProbability_zeroMolecules /usr/lib/python3/dist-packages/numpy/core/_methods.py:129: RuntimeWarning: invalid value encountered in scalar divide ret = ret.dtype.type(ret / rcount) MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_count_by_type MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_no_hydrogen_bonds /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py:733: UserWarning: No hydrogen bonds were found given d-a cutoff of 3.0 between Donor, type O, and Acceptor, type O. warnings.warn( MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_count_by_type /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py:765: UserWarning: No hydrogen bonds were found given angle of 120.0 between Donor, type O, and Acceptor, type O. warnings.warn( MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py: 10 warnings /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py:733: UserWarning: No hydrogen bonds were found given d-a cutoff of 3.0 between Donor, None, and Acceptor, name OH2. warnings.warn( MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py: 10 warnings /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py:765: UserWarning: No hydrogen bonds were found given angle of 120.0 between Donor, None, and Acceptor, name OH2. warnings.warn( MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py:355: UserWarning: donors_sel is an empty selection string - no hydrogen bonds will be found. This may be intended, but please check your selection. warnings.warn(msg.format(sel)) MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py:355: UserWarning: hydrogens_sel is an empty selection string - no hydrogen bonds will be found. This may be intended, but please check your selection. warnings.warn(msg.format(sel)) MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py:355: UserWarning: acceptors_sel is an empty selection string - no hydrogen bonds will be found. This may be intended, but please check your selection. warnings.warn(msg.format(sel)) MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py: 23 warnings /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/core/groups.py:3218: UserWarning: Empty string to select atoms, empty group returned. warnings.warn("Empty string to select atoms, empty group returned.", MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py: 10 warnings /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py:733: UserWarning: No hydrogen bonds were found given d-a cutoff of 3.0 between Donor, , and Acceptor, . warnings.warn( MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py: 10 warnings /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py:765: UserWarning: No hydrogen bonds were found given angle of 150 between Donor, , and Acceptor, . warnings.warn( MDAnalysisTests/analysis/test_leaflet.py::TestLeafletFinder::test_write_selection /build/reproducible-path/mdanalysis-2.7.0/testsuite/MDAnalysisTests/analysis/test_leaflet.py:175: ResourceWarning: unclosed file <_io.TextIOWrapper name='leaflet.vmd' mode='r' encoding='utf-8'> assert self.lines2one(open('leaflet.vmd').readlines()) == expected_output Enable tracemalloc to get traceback where the object was allocated. See https://docs.pytest.org/en/stable/how-to/capture-warnings.html#resource-warnings for more info. MDAnalysisTests/analysis/test_msd.py: 100 warnings MDAnalysisTests/analysis/test_pca.py: 100 warnings /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/topology/PDBParser.py:348: UserWarning: Unknown element X found for some atoms. These have been given an empty element record. If needed they can be guessed using MDAnalysis.topology.guessers. warnings.warn(wmsg) MDAnalysisTests/analysis/test_nuclinfo.py::test_phase_cp[RNAA-9-3.16497] MDAnalysisTests/analysis/test_nuclinfo.py::test_phase_cp[RNAA-9-3.16497] MDAnalysisTests/analysis/test_nuclinfo.py::test_phase_cp[RNAA-21-22.07721] MDAnalysisTests/analysis/test_nuclinfo.py::test_phase_cp[RNAA-21-22.07721] /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/analysis/nuclinfo.py:302: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performing this operation. (Deprecated NumPy 1.25.) phase_ang = (atan2(D, C) + (pi / 2.)) * 180. / pi MDAnalysisTests/analysis/test_psa.py::TestPSAnalysis::test_dist_mat_to_vec_i_greater_j /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/analysis/psa.py:733: UserWarning: Column index entered (j = 3 is smaller than row index (i = 4). Using symmetric element in upper triangle of distance matrix instead: i --> j, j --> i warnings.warn("Column index entered (j = {:d} is smaller than row " MDAnalysisTests/analysis/test_rdf.py::test_ignore_same_residues[residue-8] MDAnalysisTests/analysis/test_rdf.py::test_ignore_same_residues[segment-0] MDAnalysisTests/analysis/test_rdf.py::test_ignore_same_residues[chain-8] /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/analysis/rdf.py:347: DeprecationWarning: The `rdf` attribute was deprecated in MDAnalysis 2.0.0 and will be removed in MDAnalysis 3.0.0. Please use `results.rdf` instead warnings.warn(wmsg, DeprecationWarning) MDAnalysisTests/analysis/test_rdf_s.py: 13 warnings /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/analysis/rdf.py:554: DeprecationWarning: The `u` attribute is superflous and will be removed in MDAnalysis 3.0.0. warnings.warn("The `u` attribute is superflous and will be removed " MDAnalysisTests/analysis/test_rdf_s.py::test_density[True-0.021915460340071267] MDAnalysisTests/analysis/test_rdf_s.py::test_overwrite_norm /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/analysis/rdf.py:567: DeprecationWarning: The `density` attribute was deprecated in MDAnalysis 2.3.0 and will be removed in MDAnalysis 3.0.0. Please use `norm=density` instead. warnings.warn("The `density` attribute was deprecated in " MDAnalysisTests/analysis/test_wbridge.py::TestWaterBridgeAnalysis::test_nodata /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py:1782: MissingDataWarning: No data computed, do run() first. warnings.warn(msg, category=MissingDataWarning) MDAnalysisTests/auxiliary/test_core.py: 1 warning MDAnalysisTests/auxiliary/test_xvg.py: 30 warnings /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/auxiliary/base.py:175: UserWarning: AuxStep does not support time selection. Reverting to default warnings.warn("{} does not support time selection. Reverting to " MDAnalysisTests/auxiliary/test_xvg.py: 50 warnings /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/auxiliary/base.py:211: UserWarning: AuxStep does not support data selection. Reverting to default warnings.warn("{} does not support data selection. Reverting to " MDAnalysisTests/coordinates/test_chainreader.py::TestChainReaderFormats::test_set_all_formats MDAnalysisTests/coordinates/test_copying.py::test_reader_independent_iteration[ref_reader12] /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: Traceback (most recent call last): File "/build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/base.py", line 1532, in __del__ self.close() File "/build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/chain.py", line 597, in close self._apply('close') File "/build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/chain.py", line 504, in _apply return [reader.__getattribute__(method)(**kwargs) for reader in self.readers] ^^^^^^^^^^^^ AttributeError: 'ChainReader' object has no attribute 'readers' warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) MDAnalysisTests/coordinates/test_chainreader.py::TestChainReaderContinuous::test_missing MDAnalysisTests/coordinates/test_trc.py::TestTRCReaderVacuumBox::test_initial_frame_is_0 /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/chain.py:349: UserWarning: Missing frame in continuous chain warnings.warn("Missing frame in continuous chain", UserWarning) MDAnalysisTests/coordinates/test_crd.py::TestCRDWriterMissingAttrs::test_write[resnames] /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/CRD.py:248: UserWarning: Supplied AtomGroup was missing the following attributes: resnames, tempfactors. These will be written with default values. warnings.warn( MDAnalysisTests/coordinates/test_crd.py::TestCRDWriterMissingAttrs::test_write[resids] /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/CRD.py:248: UserWarning: Supplied AtomGroup was missing the following attributes: resids, tempfactors. These will be written with default values. warnings.warn( MDAnalysisTests/coordinates/test_crd.py::TestCRDWriterMissingAttrs::test_write[names] /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/CRD.py:248: UserWarning: Supplied AtomGroup was missing the following attributes: names, tempfactors. These will be written with default values. warnings.warn( MDAnalysisTests/coordinates/test_crd.py::TestCRDWriterMissingAttrs::test_write[tempfactors] /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/CRD.py:248: UserWarning: Supplied AtomGroup was missing the following attributes: tempfactors, tempfactors. These will be written with default values. warnings.warn( MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_timeseries_asel_shape[index 1] MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_timeseries_asel_shape[index 2] MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_timeseries_asel_shape[index 1 to 3] MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_timeseries_empty_asel MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_timeseries_atomgroup_asel_mutex MDAnalysisTests/coordinates/test_dcd.py::test_timeseries_atomindices[indices0] MDAnalysisTests/coordinates/test_dcd.py::test_timeseries_atomindices[indices1] MDAnalysisTests/coordinates/test_dcd.py::test_timeseries_atomindices[indices2] MDAnalysisTests/coordinates/test_memory.py::TestMemoryReader::test_filename_array /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/DCD.py:326: DeprecationWarning: asel argument to timeseries will be renamed to'atomgroup' in 3.0, see #3911 warnings.warn( MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_empty_dcd /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: Traceback (most recent call last): File "/build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/base.py", line 1532, in __del__ self.close() File "/build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/DCD.py", line 181, in close self._file.close() ^^^^^^^^^^ AttributeError: 'DCDReader' object has no attribute '_file' warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) MDAnalysisTests/coordinates/test_dcd.py::TestDCDWriter::test_no_container MDAnalysisTests/coordinates/test_dcd.py::test_write_no_natoms MDAnalysisTests/coordinates/test_lammps.py::TestLAMMPSDCDWriterClass::test_wrong_time_unit MDAnalysisTests/coordinates/test_lammps.py::TestLAMMPSDCDWriterClass::test_wrong_unit /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: Traceback (most recent call last): File "/build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/DCD.py", line 482, in __del__ self.close() File "/build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/DCD.py", line 479, in close self._file.close() ^^^^^^^^^^ AttributeError: 'DCDWriter' object has no attribute '_file' warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) MDAnalysisTests/coordinates/test_dcd.py: 2 warnings MDAnalysisTests/coordinates/test_netcdf.py: 108 warnings MDAnalysisTests/coordinates/test_timestep_api.py: 5 warnings MDAnalysisTests/coordinates/test_trj.py: 3 warnings MDAnalysisTests/coordinates/test_windows.py: 2 warnings MDAnalysisTests/core/test_atomselections.py: 3 warnings MDAnalysisTests/topology/test_top.py: 63 warnings MDAnalysisTests/topology/test_topology_str_types.py: 10 warnings /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/topology/TOPParser.py:299: UserWarning: ATOMIC_NUMBER record not found, elements attribute will not be populated. If needed these can be guessed using MDAnalysis.topology.guessers. warnings.warn(msg) MDAnalysisTests/coordinates/test_fhiaims.py::TestFHIAIMSWriter::test_writer_no_atom_names MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[FHIAIMSWriter] MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[FHIAIMSWriter] /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/FHIAIMS.py:281: UserWarning: Supplied AtomGroup was missing the following attributes: names, ids. These will be written with default values. warnings.warn( MDAnalysisTests/coordinates/test_gro.py: 20 warnings MDAnalysisTests/coordinates/test_h5md.py: 5 warnings MDAnalysisTests/coordinates/test_xdr.py: 10 warnings MDAnalysisTests/coordinates/test_xyz.py: 10 warnings /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/base.py:1034: DeprecationWarning: asel argument to timeseries will be renamed to'atomgroup' in 3.0, see #3911 warnings.warn( MDAnalysisTests/coordinates/test_gro.py::TestGROWriter::test_write_no_resnames /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/GRO.py:421: UserWarning: Supplied AtomGroup was missing the following attributes: resnames. These will be written with default values. Alternatively these can be supplied as keyword arguments. warnings.warn( MDAnalysisTests/coordinates/test_gro.py: 4 warnings MDAnalysisTests/coordinates/test_writer_api.py: 2 warnings MDAnalysisTests/core/test_atomgroup.py: 8 warnings /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/GRO.py:479: UserWarning: missing dimension - setting unit cell to zeroed box [0., 0., 0.] warnings.warn(wmsg) MDAnalysisTests/coordinates/test_gro.py: 3 warnings MDAnalysisTests/core/test_atomgroup.py: 8 warnings /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/GRO.py:228: UserWarning: Empty box [0., 0., 0.] found - treating as missing unit cell. Dimensions set to `None`. warnings.warn(wmsg) MDAnalysisTests/coordinates/test_gro.py::TestGROWriter::test_write_no_resids /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/GRO.py:421: UserWarning: Supplied AtomGroup was missing the following attributes: resids. These will be written with default values. Alternatively these can be supplied as keyword arguments. warnings.warn( MDAnalysisTests/coordinates/test_gro.py::TestGROWriter::test_writer_no_atom_names /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/GRO.py:421: UserWarning: Supplied AtomGroup was missing the following attributes: names. These will be written with default values. Alternatively these can be supplied as keyword arguments. warnings.warn( MDAnalysisTests/coordinates/test_gro.py: 95 warnings /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/GRO.py:216: UserWarning: Not all velocities were present. Unset velocities set to zero. warnings.warn("Not all velocities were present. " MDAnalysisTests/coordinates/test_gro.py::test_growriter_resid_truncation /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/GRO.py:421: UserWarning: Supplied AtomGroup was missing the following attributes: names, resnames. These will be written with default values. Alternatively these can be supplied as keyword arguments. warnings.warn( MDAnalysisTests/coordinates/test_h5md.py::TestH5MDReaderWithRealTrajectory::test_wrong_driver /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: Traceback (most recent call last): File "/build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/base.py", line 1532, in __del__ self.close() File "/build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/H5MD.py", line 739, in close self._file.close() ^^^^^^^^^^ AttributeError: 'H5MDReader' object has no attribute '_file' warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) MDAnalysisTests/coordinates/test_h5md.py: 3 warnings MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings MDAnalysisTests/coordinates/test_pdb.py: 17 warnings MDAnalysisTests/coordinates/test_trz.py: 1 warning MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings MDAnalysisTests/core/test_atomgroup.py: 15 warnings MDAnalysisTests/transformations/test_nojump.py: 1 warning MDAnalysisTests/utils/test_modelling.py: 2 warnings /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'altLocs' Using default value of ' ' warnings.warn("Found no information for attr: '{}'" MDAnalysisTests/coordinates/test_h5md.py: 3 warnings MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings MDAnalysisTests/coordinates/test_pdb.py: 17 warnings MDAnalysisTests/coordinates/test_trz.py: 1 warning MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings MDAnalysisTests/core/test_atomgroup.py: 15 warnings MDAnalysisTests/transformations/test_nojump.py: 1 warning MDAnalysisTests/utils/test_modelling.py: 2 warnings /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'icodes' Using default value of ' ' warnings.warn("Found no information for attr: '{}'" MDAnalysisTests/coordinates/test_h5md.py: 3 warnings MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings MDAnalysisTests/coordinates/test_pdb.py: 17 warnings MDAnalysisTests/coordinates/test_trz.py: 1 warning MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings MDAnalysisTests/core/test_atomgroup.py: 15 warnings MDAnalysisTests/transformations/test_nojump.py: 1 warning MDAnalysisTests/utils/test_modelling.py: 2 warnings /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'occupancies' Using default value of '1.0' warnings.warn("Found no information for attr: '{}'" MDAnalysisTests/coordinates/test_h5md.py: 3 warnings MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings MDAnalysisTests/coordinates/test_pdb.py: 17 warnings MDAnalysisTests/coordinates/test_trz.py: 1 warning MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings MDAnalysisTests/core/test_atomgroup.py: 15 warnings MDAnalysisTests/transformations/test_nojump.py: 1 warning MDAnalysisTests/utils/test_modelling.py: 2 warnings /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'tempfactors' Using default value of '0.0' warnings.warn("Found no information for attr: '{}'" MDAnalysisTests/coordinates/test_h5md.py: 3 warnings MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings MDAnalysisTests/coordinates/test_pdb.py: 16 warnings MDAnalysisTests/coordinates/test_trz.py: 1 warning MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings MDAnalysisTests/core/test_atomgroup.py: 15 warnings MDAnalysisTests/transformations/test_nojump.py: 1 warning MDAnalysisTests/utils/test_modelling.py: 2 warnings /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'record_types' Using default value of 'ATOM' warnings.warn("Found no information for attr: '{}'" MDAnalysisTests/coordinates/test_h5md.py::TestH5PYNotInstalled::test_reader_no_h5py /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: Traceback (most recent call last): File "/build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/base.py", line 1530, in __del__ for aux in self.aux_list: ^^^^^^^^^^^^^ File "/build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/base.py", line 1170, in aux_list return self._auxs.keys() ^^^^^^^^^^ AttributeError: 'H5MDReader' object has no attribute '_auxs' warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) MDAnalysisTests/coordinates/test_lammps.py: 57 warnings MDAnalysisTests/coordinates/test_windows.py: 20 warnings MDAnalysisTests/topology/test_lammpsdata.py: 18 warnings /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/topology/LAMMPSParser.py:632: UserWarning: Guessed all Masses to 1.0 warnings.warn('Guessed all Masses to 1.0') MDAnalysisTests/coordinates/test_lammps.py::TestLAMMPSDCDReader::test_wrong_time_unit MDAnalysisTests/coordinates/test_lammps.py::TestLAMMPSDCDReader::test_wrong_unit /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: Traceback (most recent call last): File "/build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/base.py", line 1530, in __del__ for aux in self.aux_list: ^^^^^^^^^^^^^ File "/build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/base.py", line 1170, in aux_list return self._auxs.keys() ^^^^^^^^^^ AttributeError: 'DCDReader' object has no attribute '_auxs' warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) MDAnalysisTests/coordinates/test_memory.py::TestMemoryReader::test_timeseries_subarray_view /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/memory.py:545: DeprecationWarning: MemoryReader.timeseries inclusive `stop` indexing will be removed in 3.0 in favour of exclusive indexing warnings.warn("MemoryReader.timeseries inclusive `stop` " MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFReader4::test_chain_times MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFReader4::test_chain_times /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/TRJ.py:554: UserWarning: NCDF trajectory does not contain `time` information; `time` will be set as an increasing index warnings.warn(wmsg) MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriter::test_write_trajectory_netCDF4 MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterTZ2::test_write_trajectory_netCDF4 /build/reproducible-path/mdanalysis-2.7.0/testsuite/MDAnalysisTests/coordinates/test_netcdf.py:700: RuntimeWarning: Cannot close a netcdf_file opened with mmap=True, when netcdf_variables or arrays referring to its data still exist. All data arrays obtained from such files refer directly to data on disk, and must be copied before the file can be cleanly closed. (See netcdf_file docstring for more information on mmap.) return self._test_write_trajectory(universe, outfile) MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriter::test_write_trajectory_netcdf MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterTZ2::test_write_trajectory_netcdf MDAnalysisTests/coordinates/test_netcdf.py::TestScipyScaleFactors::test_write_read_factors_default MDAnalysisTests/coordinates/test_netcdf.py::TestScipyScaleFactors::test_write_read_write[-2.0--2.0--2.0--2.0--2.0--2.0] MDAnalysisTests/coordinates/test_netcdf.py::TestScipyScaleFactors::test_write_read_write[-2.0--2.0--2.0--2.0--2.0--2.0] MDAnalysisTests/coordinates/test_netcdf.py::TestScipyScaleFactors::test_write_read_write[1.0-1.0-1.0-1.0-1.0-1.0] MDAnalysisTests/coordinates/test_netcdf.py::TestScipyScaleFactors::test_write_read_write[1.0-1.0-1.0-1.0-1.0-1.0] MDAnalysisTests/coordinates/test_netcdf.py::TestScipyScaleFactors::test_write_read_write[2.0-4.0-8.0-16.0-32.0-64.0] MDAnalysisTests/coordinates/test_netcdf.py::TestScipyScaleFactors::test_write_read_write[2.0-4.0-8.0-16.0-32.0-64.0] /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/TRJ.py:969: UserWarning: Could not find netCDF4 module. Falling back to MUCH slower scipy.io.netcdf implementation for writing. warnings.warn(wmsg) MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriter::test_write_trajectory_netcdf MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterTZ2::test_write_trajectory_netcdf /build/reproducible-path/mdanalysis-2.7.0/testsuite/MDAnalysisTests/coordinates/test_netcdf.py:711: RuntimeWarning: Cannot close a netcdf_file opened with mmap=True, when netcdf_variables or arrays referring to its data still exist. All data arrays obtained from such files refer directly to data on disk, and must be copied before the file can be cleanly closed. (See netcdf_file docstring for more information on mmap.) return self._test_write_trajectory(universe, outfile) MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings MDAnalysisTests/coordinates/test_pdb.py: 19 warnings MDAnalysisTests/coordinates/test_trz.py: 1 warning MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings MDAnalysisTests/core/test_atomgroup.py: 15 warnings MDAnalysisTests/transformations/test_nojump.py: 1 warning MDAnalysisTests/utils/test_modelling.py: 2 warnings /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'chainIDs' Using default value of '' warnings.warn("Found no information for attr: '{}'" MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings MDAnalysisTests/coordinates/test_pdb.py: 56 warnings MDAnalysisTests/coordinates/test_trz.py: 1 warning MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings MDAnalysisTests/core/test_atomgroup.py: 15 warnings MDAnalysisTests/transformations/test_nojump.py: 1 warning MDAnalysisTests/utils/test_modelling.py: 2 warnings /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/PDB.py:1200: UserWarning: Found missing chainIDs. Corresponding atoms will use value of 'X' warnings.warn("Found missing chainIDs." MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterErrorsWarnings::test_zero_atoms_VE /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: Traceback (most recent call last): File "/build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/base.py", line 1612, in __del__ self.close() File "/build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/TRJ.py", line 1184, in close if self.trjfile is not None: ^^^^^^^^^^^^ AttributeError: 'NCDFWriter' object has no attribute 'trjfile' warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) MDAnalysisTests/coordinates/test_pdb.py::TestPDBWriter::test_writer_no_resnames MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[MultiPDBWriter] MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[PDBWriter] MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[MultiPDBWriter] MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[PDBWriter] MDAnalysisTests/transformations/test_nojump.py::test_nojump_iterate_twice /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'resnames' Using default value of 'UNK' warnings.warn("Found no information for attr: '{}'" MDAnalysisTests/coordinates/test_pdb.py: 8 warnings MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings MDAnalysisTests/transformations/test_nojump.py: 1 warning /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'segids' Using default value of ' ' warnings.warn("Found no information for attr: '{}'" MDAnalysisTests/coordinates/test_pdb.py::TestPDBWriter::test_writer_no_resids MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[MultiPDBWriter] MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[PDBWriter] MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[MultiPDBWriter] MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[PDBWriter] MDAnalysisTests/transformations/test_nojump.py::test_nojump_iterate_twice /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'resids' Using default value of '1' warnings.warn("Found no information for attr: '{}'" MDAnalysisTests/coordinates/test_pdb.py: 6 warnings MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings MDAnalysisTests/transformations/test_nojump.py: 1 warning /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'names' Using default value of 'X' warnings.warn("Found no information for attr: '{}'" MDAnalysisTests/coordinates/test_pdb.py::TestPDBWriter::test_chainid_validated[@] /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/PDB.py:1196: UserWarning: Found chainIDs using unnaccepted character. Corresponding atoms will use value of 'X' warnings.warn("Found chainIDs using unnaccepted character." MDAnalysisTests/coordinates/test_pdb.py::TestPDBWriter::test_chainid_validated[AA] /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/PDB.py:1192: UserWarning: Found chainIDs with invalid length. Corresponding atoms will use value of 'X' warnings.warn("Found chainIDs with invalid length." MDAnalysisTests/coordinates/test_pdb.py::TestPDBXLSerial::test_load /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/topology/PDBParser.py:304: UserWarning: Serial numbers went over 100,000. Higher serials have been guessed warnings.warn("Serial numbers went over 100,000. " MDAnalysisTests/coordinates/test_pdb.py::TestPDBXLSerial::test_load /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/topology/PDBParser.py:423: UserWarning: Invalid atom serials were present, bonds will not be parsed warnings.warn("Invalid atom serials were present, bonds will not" MDAnalysisTests/coordinates/test_pdb.py::TestPDBXLSerial::test_load /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/topology/PDBParser.py:215: UserWarning: Invalid atom serials were present, bonds will not be parsed warnings.warn("Invalid atom serials were present, " MDAnalysisTests/coordinates/test_pdb.py::TestWriterAlignments::test_atomname_alignment MDAnalysisTests/coordinates/test_pdb.py::TestWriterAlignments::test_atomname_alignment MDAnalysisTests/topology/test_pdb.py::test_wrong_elements_warnings /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/topology/PDBParser.py:348: UserWarning: Unknown element found for some atoms. These have been given an empty element record. If needed they can be guessed using MDAnalysis.topology.guessers. warnings.warn(wmsg) MDAnalysisTests/coordinates/test_pdb.py::test_partially_missing_cryst /build/reproducible-path/mdanalysis-2.7.0/testsuite/MDAnalysisTests/coordinates/test_pdb.py:1240: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/reproducible-path/mdanalysis-2.7.0/testsuite/MDAnalysisTests/data/incomplete.pdb' mode='r' encoding='utf-8'> raw = open(INC_PDB, 'r').readlines() Enable tracemalloc to get traceback where the object was allocated. See https://docs.pytest.org/en/stable/how-to/capture-warnings.html#resource-warnings for more info. MDAnalysisTests/coordinates/test_pdbqt.py::TestPDBQTWriter::test_write_no_chainids_with_segids /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/PDBQT.py:296: UserWarning: Supplied AtomGroup was missing the following attributes: altLocs, charges, icodes, occupancies, tempfactors. These will be written with default values. warnings.warn( MDAnalysisTests/coordinates/test_tng.py::test_pytng_not_present_raises /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: Traceback (most recent call last): File "/build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/base.py", line 1530, in __del__ for aux in self.aux_list: ^^^^^^^^^^^^^ File "/build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/base.py", line 1170, in aux_list return self._auxs.keys() ^^^^^^^^^^ AttributeError: 'TNGReader' object has no attribute '_auxs' warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) MDAnalysisTests/coordinates/test_trc.py::TestTRCReaderTriclinicBox::test_trc_n_atoms MDAnalysisTests/coordinates/test_trc.py::TestTRCReaderTruncOctBox::test_universe MDAnalysisTests/coordinates/test_trc.py::TestTRCGenboxOrigin::test_universe MDAnalysisTests/coordinates/test_trc.py::TestTRCGenboxEuler::test_universe /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/TRC.py:265: UserWarning: The trajectory does not contain TIMESTEP blocks! warnings.warn( MDAnalysisTests/coordinates/test_trj.py::test_trj_no_natoms /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: Traceback (most recent call last): File "/build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/base.py", line 1532, in __del__ self.close() File "/build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/TRJ.py", line 352, in close if self.trjfile is None: ^^^^^^^^^^^^ AttributeError: 'TRJReader' object has no attribute 'trjfile' warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) MDAnalysisTests/coordinates/test_trz.py::test_deprecated_trz_writer MDAnalysisTests/coordinates/test_trz.py::TestTRZReader::test_read_zero_box MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter::test_no_box_warning MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_writer_trz_from_other MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_no_dt_warning MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[TRZWriter] MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[TRZWriter] /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/TRZ.py:551: UserWarning: Timestep didn't have the following attributes: 'pressure, pressure_tensor, total_energy, potential_energy, kinetic_energy, temperature, step', these will be set to 0 in the output trajectory warnings.warn("Timestep didn't have the following attributes: '{0}', " MDAnalysisTests/coordinates/test_trz.py::test_deprecated_trz_writer MDAnalysisTests/coordinates/test_trz.py::TestTRZReader::test_read_zero_box MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter::test_no_box_warning MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_writer_trz_from_other MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_no_dt_warning MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[TRZWriter] MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[TRZWriter] /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/TRZ.py:567: UserWarning: Timestep didn't have velocity information, this will be set to zero in output trajectory. warnings.warn("Timestep didn't have velocity information, " MDAnalysisTests/coordinates/test_trz.py::TestTRZReader::test_read_zero_box MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[TRZWriter] MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[TRZWriter] /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/TRZ.py:559: UserWarning: Timestep didn't have dimensions information, box will be written as all zero values warnings.warn("Timestep didn't have dimensions information, " MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter::test_long_title /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: Traceback (most recent call last): File "/build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/base.py", line 1612, in __del__ self.close() File "/build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/TRZ.py", line 605, in close if self.trzfile is None: ^^^^^^^^^^^^ AttributeError: 'TRZWriter' object has no attribute 'trzfile' warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) MDAnalysisTests/coordinates/test_writer_api.py::test_ts_error[TRZWriter] MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[TRZWriter] MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[TRZWriter] /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/TRZ.py:428: DeprecationWarning: The TRZ writer is deprecated and will be removed in MDAnalysis version 3.0.0 warnings.warn(wmsg, DeprecationWarning) MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[CRDWriter] MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[CRDWriter] /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/CRD.py:248: UserWarning: Supplied AtomGroup was missing the following attributes: resnames, resids, names, tempfactors, tempfactors. These will be written with default values. warnings.warn( MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[GROWriter] MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[GROWriter] /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/GRO.py:421: UserWarning: Supplied AtomGroup was missing the following attributes: names, resnames, resids. These will be written with default values. Alternatively these can be supplied as keyword arguments. warnings.warn( MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[PDBQTWriter] MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[PDBQTWriter] /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/PDBQT.py:296: UserWarning: Supplied AtomGroup was missing the following attributes: altLocs, charges, icodes, names, occupancies, resids, resnames, tempfactors, types, chainids. These will be written with default values. warnings.warn( MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[PQRWriter] MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[PQRWriter] /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/PQR.py:301: UserWarning: Supplied AtomGroup was missing the following attributes: names, resnames, resids, charges, radii. These will be written with default values. warnings.warn( MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[XYZWriter] MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[XYZWriter] /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/XYZ.py:193: UserWarning: Input AtomGroup or Universe does not have atom elements or names attributes, writer will default atom names to 'X' warnings.warn(wmsg) MDAnalysisTests/coordinates/test_xdr.py::TestXTCWriter_2::test_no_container /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: Traceback (most recent call last): File "/build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/XDR.py", line 324, in __del__ self.close() File "/build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/XDR.py", line 321, in close self._xdr.close() ^^^^^^^^^ AttributeError: 'XTCWriter' object has no attribute '_xdr' warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) MDAnalysisTests/coordinates/test_xdr.py::TestTRRWriter_2::test_no_container /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: Traceback (most recent call last): File "/build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/XDR.py", line 324, in __del__ self.close() File "/build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/XDR.py", line 321, in close self._xdr.close() ^^^^^^^^^ AttributeError: 'TRRWriter' object has no attribute '_xdr' warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) MDAnalysisTests/coordinates/test_xdr.py::TestXTCReader_offsets::test_reload_offsets_if_offsets_readin_io_fails MDAnalysisTests/coordinates/test_xdr.py::TestXTCReader_offsets::test_reload_offsets_if_offsets_readin_value_fails /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/XDR.py:222: UserWarning: Reading offsets from /tmp/pytest-of-pbuilder2/pytest-0/xtc0/.adk_oplsaa.xtc_offsets.npz failed, reading offsets from trajectory instead. Consider setting 'refresh_offsets=True' when loading your Universe. warnings.warn(f"Reading offsets from {fname} failed, " MDAnalysisTests/coordinates/test_xdr.py::TestXTCReader_offsets::test_persistent_offsets_readonly /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/XDR.py:202: UserWarning: Cannot write lock/offset file in same location as /tmp/pytest-of-pbuilder2/pytest-0/test_persistent_offsets_readon0/adk_oplsaa.xtc. Using slow offset calculation. warnings.warn(f"Cannot write lock/offset file in same location as " MDAnalysisTests/coordinates/test_xdr.py::TestTRRReader_offsets::test_reload_offsets_if_offsets_readin_io_fails MDAnalysisTests/coordinates/test_xdr.py::TestTRRReader_offsets::test_reload_offsets_if_offsets_readin_value_fails /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/XDR.py:222: UserWarning: Reading offsets from /tmp/pytest-of-pbuilder2/pytest-0/xtc1/.adk_oplsaa.trr_offsets.npz failed, reading offsets from trajectory instead. Consider setting 'refresh_offsets=True' when loading your Universe. warnings.warn(f"Reading offsets from {fname} failed, " MDAnalysisTests/coordinates/test_xdr.py::TestTRRReader_offsets::test_persistent_offsets_readonly /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/XDR.py:202: UserWarning: Cannot write lock/offset file in same location as /tmp/pytest-of-pbuilder2/pytest-0/test_persistent_offsets_readon0/adk_oplsaa.trr. Using slow offset calculation. warnings.warn(f"Cannot write lock/offset file in same location as " MDAnalysisTests/core/test_accumulate.py::TestAccumulate::test_accumulate_different_func[atoms] MDAnalysisTests/core/test_accumulate.py::TestAccumulate::test_accumulate_different_func[atoms] MDAnalysisTests/core/test_accumulate.py::TestAccumulate::test_accumulate_different_func[residues] MDAnalysisTests/core/test_accumulate.py::TestAccumulate::test_accumulate_different_func[residues] MDAnalysisTests/core/test_accumulate.py::TestAccumulate::test_accumulate_different_func[segments] MDAnalysisTests/core/test_accumulate.py::TestAccumulate::test_accumulate_different_func[segments] /usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:88: RuntimeWarning: overflow encountered in reduce return ufunc.reduce(obj, axis, dtype, out, **passkwargs) MDAnalysisTests/core/test_atomgroup.py: 17 warnings MDAnalysisTests/core/test_universe.py: 2 warnings /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/core/universe.py:833: DeprecationWarning: The bfactor topology attribute is only provided as an alias to the tempfactor attribute. It will be removed in 3.0. Please use the tempfactor attribute instead. warnings.warn(BFACTOR_WARNING, DeprecationWarning) MDAnalysisTests/core/test_atomgroup.py: 20 warnings MDAnalysisTests/core/test_universe.py: 4 warnings MDAnalysisTests/topology/test_mmtf.py: 3 warnings /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/core/topologyattrs.py:295: DeprecationWarning: The bfactor topology attribute is only provided as an alias to the tempfactor attribute. It will be removed in 3.0. Please use the tempfactor attribute instead. warnings.warn(BFACTOR_WARNING, DeprecationWarning) MDAnalysisTests/core/test_atomgroup.py: 13840 warnings MDAnalysisTests/core/test_wrap.py: 3 warnings /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/core/groups.py:1074: RuntimeWarning: invalid value encountered in divide return np.einsum('ij,ij->j',coords,weights[:, None]) / weights.sum() MDAnalysisTests/core/test_atomgroup.py: 59 warnings MDAnalysisTests/core/test_wrap.py: 12 warnings /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/core/groups.py:1104: RuntimeWarning: invalid value encountered in divide _centers /= _weights.sum(axis=1)[:, None] MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass -10 -3-0-selkwargs11] /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/core/selection.py:988: SelectionWarning: Using float equality to select atoms is not recommended because of inherent limitations in representing numbers on computers (see https://docs.python.org/3.8/tutorial/floatingpoint.html for more). Instead, we recommend using a range to select, e.g. 'mass -11.0 to -9.0'. If you still want to compare floats, use the `atol` and `rtol` keywords to modify the tolerance for `np.isclose`. warnings.warn(msg, category=SelectionWarning) MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass -10 -3-0-selkwargs11] /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/core/selection.py:988: SelectionWarning: Using float equality to select atoms is not recommended because of inherent limitations in representing numbers on computers (see https://docs.python.org/3.8/tutorial/floatingpoint.html for more). Instead, we recommend using a range to select, e.g. 'mass -4.0 to -2.0'. If you still want to compare floats, use the `atol` and `rtol` keywords to modify the tolerance for `np.isclose`. warnings.warn(msg, category=SelectionWarning) MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3-5-selkwargs12] MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3-5-selkwargs13] MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.30000000000000004-5-selkwargs15] MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3 0.30000000000000001-5-selkwargs16] MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3 0.30000000000000001-5-selkwargs16] MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3-10-selkwargs17] MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.30000000000000004-10-selkwargs18] MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3 0.30000000000000001-10-selkwargs19] MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3 0.30000000000000001-10-selkwargs19] /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/core/selection.py:988: SelectionWarning: Using float equality to select atoms is not recommended because of inherent limitations in representing numbers on computers (see https://docs.python.org/3.8/tutorial/floatingpoint.html for more). Instead, we recommend using a range to select, e.g. 'mass -0.7 to 1.3'. If you still want to compare floats, use the `atol` and `rtol` keywords to modify the tolerance for `np.isclose`. warnings.warn(msg, category=SelectionWarning) MDAnalysisTests/core/test_groups.py::TestDecorator::test_wrap_and_unwrap_deprecation[True-True-fragments] MDAnalysisTests/core/test_groups.py::TestDecorator::test_wrap_and_unwrap_deprecation[True-True-molecules] MDAnalysisTests/core/test_groups.py::TestDecorator::test_wrap_and_unwrap_deprecation[True-True-residues] MDAnalysisTests/core/test_groups.py::TestDecorator::test_wrap_and_unwrap_deprecation[True-True-group] MDAnalysisTests/core/test_groups.py::TestDecorator::test_wrap_and_unwrap_deprecation[True-True-segments] MDAnalysisTests/transformations/test_rotate.py::test_rotateby_atomgroup_cog_pbc MDAnalysisTests/transformations/test_rotate.py::test_rotateby_atomgroup_com_pbc MDAnalysisTests/transformations/test_translate.py::test_center_in_box_coords_all_options /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/core/groups.py:445: DeprecationWarning: The 'pbc' kwarg has been deprecated and will be removed in version 3.0., please use 'wrap' instead warnings.warn("The 'pbc' kwarg has been deprecated and will be " MDAnalysisTests/core/test_topologyattrs.py::TestDeprecateBFactor::test_deprecate_bfactor_sel /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/core/selection.py:988: SelectionWarning: Using float equality to select atoms is not recommended because of inherent limitations in representing numbers on computers (see https://docs.python.org/3.8/tutorial/floatingpoint.html for more). Instead, we recommend using a range to select, e.g. 'bfactor 2.0 to 4.0'. If you still want to compare floats, use the `atol` and `rtol` keywords to modify the tolerance for `np.isclose`. warnings.warn(msg, category=SelectionWarning) MDAnalysisTests/lib/test_distances.py::TestCythonFunctions::test_numpy_compliance_angles[serial] MDAnalysisTests/lib/test_distances.py::TestCythonFunctions::test_numpy_compliance_angles[openmp] MDAnalysisTests/lib/test_distances.py::TestCythonFunctions::test_numpy_compliance_dihedrals[serial] MDAnalysisTests/lib/test_distances.py::TestCythonFunctions::test_numpy_compliance_dihedrals[serial] MDAnalysisTests/lib/test_distances.py::TestCythonFunctions::test_numpy_compliance_dihedrals[openmp] MDAnalysisTests/lib/test_distances.py::TestCythonFunctions::test_numpy_compliance_dihedrals[openmp] MDAnalysisTests/lib/test_util.py::TestGeometryFunctions::test_vectors[x_axis5-y_axis5-nan] /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/lib/mdamath.py:156: RuntimeWarning: invalid value encountered in scalar divide x = np.dot(a, b) / (norm(a) * norm(b)) MDAnalysisTests/lib/test_util.py: 48 warnings /build/reproducible-path/mdanalysis-2.7.0/testsuite/MDAnalysisTests/lib/test_util.py:293: RuntimeWarning: invalid value encountered in sqrt ref[2, 2] = np.sqrt(z * z - ref[2, 0] ** 2 - ref[2, 1] ** 2) MDAnalysisTests/lib/test_util.py: 353 warnings /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/lib/mdamath.py:392: RuntimeWarning: invalid value encountered in sqrt box_matrix[2, 2] = np.sqrt(lz * lz - box_matrix[2, 0] ** 2 - MDAnalysisTests/lib/test_util.py: 339 warnings /build/reproducible-path/mdanalysis-2.7.0/testsuite/MDAnalysisTests/lib/test_util.py:324: RuntimeWarning: invalid value encountered in scalar divide a = np.rad2deg(np.arccos(np.dot(tri_vecs[1], tri_vecs[2]) / (y * z))) MDAnalysisTests/lib/test_util.py: 363 warnings /build/reproducible-path/mdanalysis-2.7.0/testsuite/MDAnalysisTests/lib/test_util.py:325: RuntimeWarning: invalid value encountered in scalar divide b = np.rad2deg(np.arccos(np.dot(tri_vecs[0], tri_vecs[2]) / (x * z))) MDAnalysisTests/lib/test_util.py: 756 warnings /build/reproducible-path/mdanalysis-2.7.0/testsuite/MDAnalysisTests/lib/test_util.py:326: RuntimeWarning: invalid value encountered in scalar divide c = np.rad2deg(np.arccos(np.dot(tri_vecs[0], tri_vecs[1]) / (x * y))) MDAnalysisTests/lib/test_util.py: 43 warnings /build/reproducible-path/mdanalysis-2.7.0/testsuite/MDAnalysisTests/lib/test_util.py:315: RuntimeWarning: invalid value encountered in scalar divide ref[2, 1] = z * (cos_a - cos_b * cos_c) / sin_c MDAnalysisTests/lib/test_util.py: 17 warnings /build/reproducible-path/mdanalysis-2.7.0/testsuite/MDAnalysisTests/lib/test_util.py:315: RuntimeWarning: divide by zero encountered in scalar divide ref[2, 1] = z * (cos_a - cos_b * cos_c) / sin_c MDAnalysisTests/parallelism/test_pickle_transformation.py::test_add_PositionAverager_pickle[u0] MDAnalysisTests/transformations/test_positionaveraging.py::test_posavging_fwd MDAnalysisTests/transformations/test_positionaveraging.py::test_posavging_bwd MDAnalysisTests/transformations/test_positionaveraging.py::test_posavging_reset MDAnalysisTests/transformations/test_positionaveraging.py::test_posavging_specific /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/transformations/positionaveraging.py:193: Warning: Cannot average position for non sequentialiterations. Averager will be reset. warnings.warn('Cannot average position for non sequential' MDAnalysisTests/topology/test_pdb.py::test_PDB_no_resid MDAnalysisTests/topology/test_pdb.py::test_PDB_no_resid MDAnalysisTests/topology/test_pdb.py::test_PDB_no_resid MDAnalysisTests/topology/test_pdb.py::test_PDB_no_resid /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/topology/PDBParser.py:290: UserWarning: PDB file is missing resid information. Defaulted to '1' warnings.warn("PDB file is missing resid information. " MDAnalysisTests/topology/test_top.py: 42 warnings /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/topology/TOPParser.py:306: UserWarning: Unknown ATOMIC_NUMBER value found for some atoms, these have been given an empty element record. If needed these can be guessed using MDAnalysis.topology.guessers. warnings.warn(msg) MDAnalysisTests/transformations/test_fit.py::test_fit_translation_no_masses /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/analysis/align.py:1509: SelectionWarning: Atoms could not be matched since they don't contain masses. warnings.warn(msg, category=SelectionWarning) MDAnalysisTests/transformations/test_nojump.py::test_nojump_constantvel_stride_2 /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/transformations/nojump.py:139: UserWarning: NoJump detected that the interval between frames is unequal.We are resetting the reference frame to the current timestep. warnings.warn( MDAnalysisTests/utils/test_pickleio.py::test_get_right_open_handler_text[f_text0] MDAnalysisTests/utils/test_pickleio.py::test_get_right_open_handler_text[f_text1] MDAnalysisTests/utils/test_pickleio.py::test_iopickle_text[f_text0] MDAnalysisTests/utils/test_pickleio.py::test_iopickle_text[f_text1] MDAnalysisTests/utils/test_pickleio.py::test_offset_text_to_0[f_text0] MDAnalysisTests/utils/test_pickleio.py::test_offset_text_to_0[f_text1] /usr/lib/python3/dist-packages/_pytest/runner.py:142: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/reproducible-path/mdanalysis-2.7.0/testsuite/MDAnalysisTests/data/adk_oplsaa.pdb' encoding='utf-8'> item.funcargs = None # type: ignore[attr-defined] Enable tracemalloc to get traceback where the object was allocated. See https://docs.pytest.org/en/stable/how-to/capture-warnings.html#resource-warnings for more info. MDAnalysisTests/utils/test_pickleio.py::test_iopickle_text[f_text0] MDAnalysisTests/utils/test_pickleio.py::test_iopickle_text[f_text1] MDAnalysisTests/utils/test_pickleio.py::test_offset_text_to_0[f_text0] MDAnalysisTests/utils/test_pickleio.py::test_offset_text_to_0[f_text1] MDAnalysisTests/utils/test_pickleio.py::test_context_manager_pickle /usr/lib/python3/dist-packages/_pytest/python.py:159: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/reproducible-path/mdanalysis-2.7.0/testsuite/MDAnalysisTests/data/adk_oplsaa.pdb' encoding='utf-8'> result = testfunction(**testargs) Enable tracemalloc to get traceback where the object was allocated. See https://docs.pytest.org/en/stable/how-to/capture-warnings.html#resource-warnings for more info. MDAnalysisTests/utils/test_pickleio.py::test_get_right_open_handler_byte[f_byte0] MDAnalysisTests/utils/test_pickleio.py::test_iopickle_byte[f_byte0] MDAnalysisTests/utils/test_pickleio.py::test_offset_byte_to_tell[f_byte0] /usr/lib/python3/dist-packages/_pytest/runner.py:142: ResourceWarning: unclosed file item.funcargs = None # type: ignore[attr-defined] Enable tracemalloc to get traceback where the object was allocated. See https://docs.pytest.org/en/stable/how-to/capture-warnings.html#resource-warnings for more info. MDAnalysisTests/utils/test_pickleio.py::test_iopickle_byte[f_byte0] MDAnalysisTests/utils/test_pickleio.py::test_offset_byte_to_tell[f_byte0] MDAnalysisTests/utils/test_pickleio.py::test_fileio_pickle MDAnalysisTests/utils/test_pickleio.py::test_fileio_pickle /usr/lib/python3/dist-packages/_pytest/python.py:159: ResourceWarning: unclosed file <_io.FileIO name='/build/reproducible-path/mdanalysis-2.7.0/testsuite/MDAnalysisTests/data/adk_oplsaa.pdb' mode='rb' closefd=True> result = testfunction(**testargs) Enable tracemalloc to get traceback where the object was allocated. See https://docs.pytest.org/en/stable/how-to/capture-warnings.html#resource-warnings for more info. MDAnalysisTests/utils/test_pickleio.py::test_pickle_with_write_mode[unpicklable_f0] /usr/lib/python3/dist-packages/_pytest/python.py:159: ResourceWarning: unclosed file <_io.FileIO name=local('/tmp/pytest-of-pbuilder2/pytest-0/test_pickle_with_write_mode_un0/pickle/test.pdb') mode='wb' closefd=True> result = testfunction(**testargs) Enable tracemalloc to get traceback where the object was allocated. See https://docs.pytest.org/en/stable/how-to/capture-warnings.html#resource-warnings for more info. MDAnalysisTests/utils/test_pickleio.py::test_pickle_with_write_mode[unpicklable_f1] /usr/lib/python3/dist-packages/_pytest/python.py:159: ResourceWarning: unclosed file <_io.FileIO name=local('/tmp/pytest-of-pbuilder2/pytest-0/test_pickle_with_write_mode_un1/pickle/test.pdb') mode='xb' closefd=True> result = testfunction(**testargs) Enable tracemalloc to get traceback where the object was allocated. See https://docs.pytest.org/en/stable/how-to/capture-warnings.html#resource-warnings for more info. MDAnalysisTests/utils/test_pickleio.py::test_pickle_with_write_mode[unpicklable_f2] /usr/lib/python3/dist-packages/_pytest/python.py:159: ResourceWarning: unclosed file <_io.FileIO name=local('/tmp/pytest-of-pbuilder2/pytest-0/test_pickle_with_write_mode_un2/pickle/test.pdb') mode='ab' closefd=True> result = testfunction(**testargs) Enable tracemalloc to get traceback where the object was allocated. See https://docs.pytest.org/en/stable/how-to/capture-warnings.html#resource-warnings for more info. MDAnalysisTests/utils/test_units.py::TestConstants::test_constant[Boltzman_constant-0.008314462159] /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/units.py:183: DeprecationWarning: Please use 'Boltzmann_constant' henceforth. The key 'Boltzman_constant' was a typo and will be removed in MDAnalysis 2.8.0. warnings.warn(wmsg, DeprecationWarning) -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html = 18631 passed, 594 skipped, 7 xfailed, 3 xpassed, 27465 warnings in 1985.99s (0:33:05) = --- Logging error --- Traceback (most recent call last): File "/usr/lib/python3/dist-packages/duecredit/utils.py", line 209, in wrapped_func return f(*args, **kwargs) ^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3/dist-packages/duecredit/dueswitch.py", line 102, in dump due_summary.dump() File "/usr/lib/python3/dist-packages/duecredit/collector.py", line 499, in dump output.dump() File "/usr/lib/python3/dist-packages/duecredit/io.py", line 247, in dump self.fd.write(get_text_rendering(cit.entry, style=self.style)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3/dist-packages/duecredit/io.py", line 254, in get_text_rendering return format_bibtex(get_bibtex_rendering(entry), style=style) ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3/dist-packages/duecredit/io.py", line 267, in get_bibtex_rendering return BibTeX(import_doi(entry.doi)) ^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3/dist-packages/duecredit/io.py", line 50, in import_doi cached = get_doi_cache_file(doi) ^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3/dist-packages/duecredit/io.py", line 43, in get_doi_cache_file os.makedirs(CACHE_DIR) File "", line 215, in makedirs File "", line 215, in makedirs File "", line 215, in makedirs [Previous line repeated 1 more time] File "", line 225, in makedirs PermissionError: [Errno 13] Permission denied: '/nonexistent' During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/usr/lib/python3.12/logging/__init__.py", line 1163, in emit stream.write(msg + self.terminator) ValueError: I/O operation on closed file. Call stack: File "/usr/lib/python3/dist-packages/duecredit/utils.py", line 211, in wrapped_func lgr.warning( Message: "DueCredit internal failure while running : PermissionError(13, 'Permission denied'). Please report to developers at https://github.com/duecredit/duecredit/issues" Arguments: () DueCredit Report: - Molecular simulation analysis library / MDAnalysis (v 2.7.0) [1, 2] - Bond-Angle-Torsions Coordinate Transformation / MDAnalysis.analysis.bat.BAT (v 2.7.0) [3] - Dielectric analysis / MDAnalysis.analysis.dielectric (v 2.7.0) [4] - ENCORE Ensemble Comparison / MDAnalysis.analysis.encore (v 2.7.0) [5] - HOLE trajectory analysis with orderparameters, HOLE program / MDAnalysis.analysis.hole2 (v 2.7.0) [6, 7, 8] - Hydrogen bond analysis implementation / MDAnalysis.analysis.hydrogenbonds.hbond_analysis (v 2.7.0) [9] - Hydrogen bonding autocorrelation time / MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel (v 2.7.0) [10] - LeafletFinder algorithm / MDAnalysis.analysis.leaflet (v 2.7.0) [2] - Mean Squared Displacements with tidynamics, FCA fast correlation algorithm / MDAnalysis.analysis.msd (v 2.7.0) [11, 12] - Cumulative overlap / MDAnalysis.analysis.pca (v 2.7.0) [13] - Path Similarity Analysis algorithm and implementation / MDAnalysis.analysis.psa (v 2.7.0) [14] - Specifications of the H5MD standard, MDAnalysis trajectory reader/writer of the H5MDformat / MDAnalysis.coordinates.H5MD (v 2.7.0, 1.1) [15, 16] - MMTF Reader / MDAnalysis.coordinates.MMTF (v 2.7.0) [17] - The TNG paper / MDAnalysis.coordinates.TNG (v 2.7.0) [18] - QCProt implementation / MDAnalysis.lib.qcprot (v 2.7.0) [19, 20] - MMTF Parser / MDAnalysis.topology.MMTFParser (v 2.7.0) [17] - Works through the orthogonal case for unwrapping, and proposes the non-orthogonal approach. / MDAnalysis.transformations.nojump (v 2.7.0) [21] - Scientific tools library / numpy (v 1.26.4) [22] 2 packages cited 16 modules cited 0 functions cited References ---------- [1] make[1]: Leaving directory '/build/reproducible-path/mdanalysis-2.7.0' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install -O--buildsystem=pybuild I: pybuild plugin_pyproject:178: Copying package built for python3.12 to destdir dh_installdocs -O--buildsystem=pybuild dh_installdocs: warning: Cannot auto-detect main package for python-mdanalysis-doc. If the default is wrong, please use --doc-main-package dh_sphinxdoc -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild dh_python3 -O--buildsystem=pybuild debian/rules execute_after_dh_python3 make[1]: Entering directory '/build/reproducible-path/mdanalysis-2.7.0' dh_numpy3 make[1]: Leaving directory '/build/reproducible-path/mdanalysis-2.7.0' dh_installsystemduser -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild dh_compress -O--buildsystem=pybuild dh_fixperms -O--buildsystem=pybuild dh_missing -O--buildsystem=pybuild dh_dwz -a -O--buildsystem=pybuild dh_strip -a -O--buildsystem=pybuild dh_makeshlibs -a -O--buildsystem=pybuild dh_shlibdeps -a -O--buildsystem=pybuild dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-armhf.so.3 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-armhf.so.3.usr-is-merged dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dpkg-gencontrol: warning: package python-mdanalysis-doc: substitution variable ${python3:Depends} unused, but is defined dpkg-gencontrol: warning: package python-mdanalysis-doc: substitution variable ${sphinxdoc:Built-Using} unused, but is defined dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'python3-mdanalysis' in '../python3-mdanalysis_2.7.0-5_armhf.deb'. dpkg-deb: building package 'python3-mdanalysis-dbgsym' in '../python3-mdanalysis-dbgsym_2.7.0-5_armhf.deb'. dpkg-deb: building package 'python-mdanalysis-doc' in '../python-mdanalysis-doc_2.7.0-5_all.deb'. dpkg-genbuildinfo --build=binary -O../mdanalysis_2.7.0-5_armhf.buildinfo dpkg-genchanges --build=binary -O../mdanalysis_2.7.0-5_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-source: info: using options from mdanalysis-2.7.0/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/1520/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/1520/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/1520 and its subdirectories I: Current time: Thu Sep 12 00:57:47 +14 2024 I: pbuilder-time-stamp: 1726052267