I: pbuilder: network access will be disabled during build I: Current time: Sun Jan 7 02:27:18 +14 2024 I: pbuilder-time-stamp: 1704544038 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [mdtraj_1.9.5-1.dsc] I: copying [./mdtraj_1.9.5.orig.tar.gz] I: copying [./mdtraj_1.9.5-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.ldC6vech/trustedkeys.kbx': General error gpgv: Signature made Mon Jan 18 05:50:28 2021 gpgv: using RSA key 23C9A93E585819E9126D0A36573EF1E4BD5A01FA gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./mdtraj_1.9.5-1.dsc dpkg-source: info: extracting mdtraj in mdtraj-1.9.5 dpkg-source: info: unpacking mdtraj_1.9.5.orig.tar.gz dpkg-source: info: unpacking mdtraj_1.9.5-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying build_dir_pybuild.patch dpkg-source: info: applying python_hashbang.patch dpkg-source: info: applying test_gsd_skip.patch dpkg-source: info: applying check_sse2.patch dpkg-source: info: applying reinstate_astor_not_astunparse_revert_a8b2b9c.patch dpkg-source: info: applying 32bit_skip_image_molecule.patch dpkg-source: info: applying test_order_relax_tol.patch dpkg-source: info: applying rename-mdconvert-mdtraj.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/4100091/tmp/hooks/D01_modify_environment starting debug: Running on ionos1-amd64. 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 Jan 6 12:28 /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/4100091/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/4100091/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.1.4(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=15 ' DIRSTACK=() DISTRIBUTION=bullseye EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=a011c5e6d72448ff96af4e9931cc8996 LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=4100091 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.ykj6IQ5s/pbuilderrc_0OcN --distribution bullseye --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ykj6IQ5s/b2 --logfile b2/build.log mdtraj_1.9.5-1.dsc' SUDO_GID=110 SUDO_UID=105 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://78.137.99.97:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-17-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.69-1 (2023-12-30) x86_64 GNU/Linux I: ls -l /bin total 5476 -rwxr-xr-x 1 root root 1234376 Mar 27 2022 bash -rwxr-xr-x 3 root root 38984 Jul 20 2020 bunzip2 -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzip2 -rwxr-xr-x 1 root root 18424 Jul 20 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore -rwxr-xr-x 1 root root 43936 Sep 24 2020 cat -rwxr-xr-x 1 root root 72672 Sep 24 2020 chgrp -rwxr-xr-x 1 root root 64448 Sep 24 2020 chmod -rwxr-xr-x 1 root root 72672 Sep 24 2020 chown -rwxr-xr-x 1 root root 151168 Sep 24 2020 cp -rwxr-xr-x 1 root root 125560 Dec 10 2020 dash -rwxr-xr-x 1 root root 113664 Sep 24 2020 date -rwxr-xr-x 1 root root 80968 Sep 24 2020 dd -rwxr-xr-x 1 root root 93936 Sep 24 2020 df -rwxr-xr-x 1 root root 147176 Sep 24 2020 dir -rwxr-xr-x 1 root root 84440 Jan 20 2022 dmesg lrwxrwxrwx 1 root root 8 Nov 7 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 7 2019 domainname -> hostname -rwxr-xr-x 1 root root 39712 Sep 24 2020 echo -rwxr-xr-x 1 root root 28 Jan 25 2023 egrep -rwxr-xr-x 1 root root 39680 Sep 24 2020 false -rwxr-xr-x 1 root root 28 Jan 25 2023 fgrep -rwxr-xr-x 1 root root 69032 Jan 20 2022 findmnt -rwsr-xr-x 1 root root 34896 Feb 26 2021 fusermount -rwxr-xr-x 1 root root 203072 Jan 25 2023 grep -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe -rwxr-xr-x 1 root root 98048 Apr 10 2022 gzip -rwxr-xr-x 1 root root 22600 Nov 7 2019 hostname -rwxr-xr-x 1 root root 72840 Sep 24 2020 ln -rwxr-xr-x 1 root root 56952 Feb 7 2020 login -rwxr-xr-x 1 root root 147176 Sep 24 2020 ls -rwxr-xr-x 1 root root 149736 Jan 20 2022 lsblk -rwxr-xr-x 1 root root 85184 Sep 24 2020 mkdir -rwxr-xr-x 1 root root 76896 Sep 24 2020 mknod -rwxr-xr-x 1 root root 48064 Sep 24 2020 mktemp -rwxr-xr-x 1 root root 59632 Jan 20 2022 more -rwsr-xr-x 1 root root 55528 Jan 20 2022 mount -rwxr-xr-x 1 root root 18664 Jan 20 2022 mountpoint -rwxr-xr-x 1 root root 147080 Sep 24 2020 mv lrwxrwxrwx 1 root root 8 Nov 7 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Dec 16 2021 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43872 Sep 24 2020 pwd lrwxrwxrwx 1 root root 4 Mar 27 2022 rbash -> bash -rwxr-xr-x 1 root root 52032 Sep 24 2020 readlink -rwxr-xr-x 1 root root 72704 Sep 24 2020 rm -rwxr-xr-x 1 root root 52032 Sep 24 2020 rmdir -rwxr-xr-x 1 root root 27472 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed lrwxrwxrwx 1 root root 9 Jan 6 12:28 sh -> /bin/bash -rwxr-xr-x 1 root root 43808 Sep 24 2020 sleep -rwxr-xr-x 1 root root 84928 Sep 24 2020 stty -rwsr-xr-x 1 root root 71912 Jan 20 2022 su -rwxr-xr-x 1 root root 39744 Sep 24 2020 sync -rwxr-xr-x 1 root root 531928 Feb 17 2021 tar -rwxr-xr-x 1 root root 14456 Sep 27 2020 tempfile -rwxr-xr-x 1 root root 101408 Sep 24 2020 touch -rwxr-xr-x 1 root root 39680 Sep 24 2020 true -rwxr-xr-x 1 root root 14328 Feb 26 2021 ulockmgr_server -rwsr-xr-x 1 root root 35040 Jan 20 2022 umount -rwxr-xr-x 1 root root 39744 Sep 24 2020 uname -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress -rwxr-xr-x 1 root root 147176 Sep 24 2020 vdir -rwxr-xr-x 1 root root 63744 Jan 20 2022 wdctl lrwxrwxrwx 1 root root 8 Nov 7 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp -rwxr-xr-x 1 root root 5898 Apr 10 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce -rwxr-xr-x 1 root root 8049 Apr 10 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew I: user script /srv/workspace/pbuilder/4100091/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: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-python, cython3 (>= 0.29~), python3-setuptools, python3-all-dev, python3-numpy (>= 1.6~), python3-scipy, python3-astor, python3-networkx, python3-pandas, python3-pyparsing, python3-sphinx, python3-tables, libjs-mathjax, python3-msmb-theme, python3-ipykernel, python3-jupyter-client, python3-matplotlib, python3-nbconvert, python3-nbformat, python3-numpydoc, python3-six, python3-sklearn dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 17743 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on cython3 (>= 0.29~); however: Package cython3 is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-all-dev; however: Package python3-all-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-numpy (>= 1.6~); however: Package python3-numpy is not installed. pbuilder-satisfydepends-dummy depends on python3-scipy; however: Package python3-scipy is not installed. pbuilder-satisfydepends-dummy depends on python3-astor; however: Package python3-astor is not installed. pbuilder-satisfydepends-dummy depends on python3-networkx; however: Package python3-networkx is not installed. pbuilder-satisfydepends-dummy depends on python3-pandas; however: Package python3-pandas is not installed. pbuilder-satisfydepends-dummy depends on python3-pyparsing; however: Package python3-pyparsing is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx; however: Package python3-sphinx is not installed. pbuilder-satisfydepends-dummy depends on python3-tables; however: Package python3-tables is not installed. pbuilder-satisfydepends-dummy depends on libjs-mathjax; however: Package libjs-mathjax is not installed. pbuilder-satisfydepends-dummy depends on python3-msmb-theme; however: Package python3-msmb-theme is not installed. pbuilder-satisfydepends-dummy depends on python3-ipykernel; however: Package python3-ipykernel is not installed. pbuilder-satisfydepends-dummy depends on python3-jupyter-client; however: Package python3-jupyter-client is not installed. pbuilder-satisfydepends-dummy depends on python3-matplotlib; however: Package python3-matplotlib is not installed. pbuilder-satisfydepends-dummy depends on python3-nbconvert; however: Package python3-nbconvert is not installed. pbuilder-satisfydepends-dummy depends on python3-nbformat; however: Package python3-nbformat is not installed. pbuilder-satisfydepends-dummy depends on python3-numpydoc; however: Package python3-numpydoc is not installed. pbuilder-satisfydepends-dummy depends on python3-six; however: Package python3-six is not installed. pbuilder-satisfydepends-dummy depends on python3-sklearn; however: Package python3-sklearn is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} 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} fonts-font-awesome{a} fonts-lato{a} fonts-lyx{a} fonts-mathjax{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libaec0{a} libarchive-zip-perl{a} libblas3{a} libblosc1{a} libbrotli1{a} libbsd0{a} libdebhelper-perl{a} libdeflate0{a} libelf1{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libfreetype6{a} libgfortran5{a} libhdf5-103-1{a} libicu67{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-jquery-ui{a} libjs-mathjax{a} libjs-sphinxdoc{a} libjs-underscore{a} liblapack3{a} liblbfgsb0{a} liblcms2-2{a} liblzo2-2{a} libmagic-mgc{a} libmagic1{a} libmd0{a} libmpdec3{a} libncurses6{a} libnorm1{a} libpgm-5.3-0{a} libpipeline1{a} libpng16-16{a} libprocps8{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.9{a} libpython3.9-dev{a} libpython3.9-minimal{a} libpython3.9-stdlib{a} libreadline8{a} libsigsegv2{a} libsnappy1v5{a} libsodium23{a} libsub-override-perl{a} libsz2{a} libtiff5{a} libtool{a} libuchardet0{a} libwebp6{a} libwebpdemux2{a} libwebpmux3{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxml2{a} libzmq5{a} m4{a} mailcap{a} man-db{a} media-types{a} mime-support{a} openssl{a} po-debconf{a} procps{a} python-babel-localedata{a} python-matplotlib-data{a} python-tables-data{a} python3{a} python3-alabaster{a} python3-all{a} python3-all-dev{a} python3-astor{a} python3-attr{a} python3-babel{a} python3-backcall{a} python3-bleach{a} python3-certifi{a} python3-chardet{a} python3-cycler{a} python3-dateutil{a} python3-decorator{a} python3-defusedxml{a} python3-dev{a} python3-distutils{a} python3-docutils{a} python3-entrypoints{a} python3-html5lib{a} python3-idna{a} python3-imagesize{a} python3-importlib-metadata{a} python3-ipykernel{a} python3-ipython{a} python3-ipython-genutils{a} python3-jedi{a} python3-jinja2{a} python3-joblib{a} python3-jsonschema{a} python3-jupyter-client{a} python3-jupyter-core{a} python3-kiwisolver{a} python3-lib2to3{a} python3-markupsafe{a} python3-matplotlib{a} python3-minimal{a} python3-mistune{a} python3-more-itertools{a} python3-msmb-theme{a} python3-nbconvert{a} python3-nbformat{a} python3-networkx{a} python3-numexpr{a} python3-numpy{a} python3-numpydoc{a} python3-packaging{a} python3-pandas{a} python3-pandas-lib{a} python3-pandocfilters{a} python3-parso{a} python3-pexpect{a} python3-pickleshare{a} python3-pil{a} python3-pkg-resources{a} python3-prompt-toolkit{a} python3-ptyprocess{a} python3-pygments{a} python3-pyparsing{a} python3-pyrsistent{a} python3-requests{a} python3-roman{a} python3-scipy{a} python3-setuptools{a} python3-six{a} python3-sklearn{a} python3-sklearn-lib{a} python3-snowballstemmer{a} python3-sphinx{a} python3-sphinx-rtd-theme{a} python3-tables{a} python3-tables-lib{a} python3-testpath{a} python3-threadpoolctl{a} python3-tornado{a} python3-traitlets{a} python3-tz{a} python3-urllib3{a} python3-wcwidth{a} python3-webencodings{a} python3-zipp{a} python3-zmq{a} python3.9{a} python3.9-dev{a} python3.9-minimal{a} readline-common{a} sensible-utils{a} sgml-base{a} sphinx-common{a} sphinx-rtd-theme-common{a} ttf-bitstream-vera{a} tzdata{a} xml-core{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl javascript-common libarchive-cpio-perl libgpm2 libltdl-dev libmail-sendmail-perl libpaper-utils lynx pandoc psmisc python3-bottleneck python3-bs4 python3-gdal python3-lxml python3-nose python3-numba python3-odf python3-olefile python3-openpyxl python3-psutil python3-pydot python3-pygraphviz python3-pytest python3-simplejson python3-tk python3-xlwt python3-yaml wget 0 packages upgraded, 189 newly installed, 0 to remove and 0 not upgraded. Need to get 102 MB of archives. After unpacking 441 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main amd64 bsdextrautils amd64 2.36.1-8+deb11u1 [145 kB] Get: 2 http://deb.debian.org/debian bullseye/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 3 http://deb.debian.org/debian bullseye/main amd64 groff-base amd64 1.22.4-6 [936 kB] Get: 4 http://deb.debian.org/debian bullseye/main amd64 libpipeline1 amd64 1.5.3-1 [34.3 kB] Get: 5 http://deb.debian.org/debian bullseye/main amd64 man-db amd64 2.9.4-2 [1354 kB] Get: 6 http://deb.debian.org/debian bullseye/main amd64 fonts-lato all 2.0-2.1 [2696 kB] Get: 7 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-minimal amd64 3.9.2-1 [801 kB] Get: 8 http://deb.debian.org/debian bullseye/main amd64 libexpat1 amd64 2.2.10-2+deb11u5 [98.2 kB] Get: 9 http://deb.debian.org/debian bullseye/main amd64 python3.9-minimal amd64 3.9.2-1 [1955 kB] Get: 10 http://deb.debian.org/debian bullseye/main amd64 python3-minimal amd64 3.9.2-3 [38.2 kB] Get: 11 http://deb.debian.org/debian bullseye/main amd64 media-types all 4.0.0 [30.3 kB] Get: 12 http://deb.debian.org/debian bullseye/main amd64 mailcap all 3.69 [31.7 kB] Get: 13 http://deb.debian.org/debian bullseye/main amd64 mime-support all 3.66 [10.9 kB] Get: 14 http://deb.debian.org/debian bullseye/main amd64 tzdata all 2021a-1+deb11u10 [286 kB] Get: 15 http://deb.debian.org/debian bullseye/main amd64 libmpdec3 amd64 2.5.1-1 [87.7 kB] Get: 16 http://deb.debian.org/debian bullseye/main amd64 readline-common all 8.1-1 [73.7 kB] Get: 17 http://deb.debian.org/debian bullseye/main amd64 libreadline8 amd64 8.1-1 [169 kB] Get: 18 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-stdlib amd64 3.9.2-1 [1684 kB] Get: 19 http://deb.debian.org/debian bullseye/main amd64 python3.9 amd64 3.9.2-1 [466 kB] Get: 20 http://deb.debian.org/debian bullseye/main amd64 libpython3-stdlib amd64 3.9.2-3 [21.4 kB] Get: 21 http://deb.debian.org/debian bullseye/main amd64 python3 amd64 3.9.2-3 [37.9 kB] Get: 22 http://deb.debian.org/debian bullseye/main amd64 sgml-base all 1.30 [15.1 kB] Get: 23 http://deb.debian.org/debian bullseye/main amd64 libncurses6 amd64 6.2+20201114-2+deb11u2 [102 kB] Get: 24 http://deb.debian.org/debian bullseye/main amd64 libprocps8 amd64 2:3.3.17-5 [63.9 kB] Get: 25 http://deb.debian.org/debian bullseye/main amd64 procps amd64 2:3.3.17-5 [502 kB] Get: 26 http://deb.debian.org/debian bullseye/main amd64 sensible-utils all 0.0.14 [14.8 kB] Get: 27 http://deb.debian.org/debian bullseye/main amd64 openssl amd64 1.1.1w-0+deb11u1 [859 kB] Get: 28 http://deb.debian.org/debian bullseye/main amd64 ca-certificates all 20210119 [158 kB] Get: 29 http://deb.debian.org/debian bullseye/main amd64 libmagic-mgc amd64 1:5.39-3+deb11u1 [273 kB] Get: 30 http://deb.debian.org/debian bullseye/main amd64 libmagic1 amd64 1:5.39-3+deb11u1 [128 kB] Get: 31 http://deb.debian.org/debian bullseye/main amd64 file amd64 1:5.39-3+deb11u1 [69.2 kB] Get: 32 http://deb.debian.org/debian bullseye/main amd64 gettext-base amd64 0.21-4 [175 kB] Get: 33 http://deb.debian.org/debian bullseye/main amd64 libsigsegv2 amd64 2.13-1 [34.8 kB] Get: 34 http://deb.debian.org/debian bullseye/main amd64 m4 amd64 1.4.18-5 [204 kB] Get: 35 http://deb.debian.org/debian bullseye/main amd64 autoconf all 2.69-14 [313 kB] Get: 36 http://deb.debian.org/debian bullseye/main amd64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 37 http://deb.debian.org/debian bullseye/main amd64 automake all 1:1.16.3-2 [814 kB] Get: 38 http://deb.debian.org/debian bullseye/main amd64 autopoint all 0.21-4 [510 kB] Get: 39 http://deb.debian.org/debian bullseye/main amd64 cython3 amd64 0.29.21-3+b1 [1312 kB] Get: 40 http://deb.debian.org/debian bullseye/main amd64 libdebhelper-perl all 13.3.4 [189 kB] Get: 41 http://deb.debian.org/debian bullseye/main amd64 libtool all 2.4.6-15 [513 kB] Get: 42 http://deb.debian.org/debian bullseye/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 43 http://deb.debian.org/debian bullseye/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 44 http://deb.debian.org/debian bullseye/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get: 45 http://deb.debian.org/debian bullseye/main amd64 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 46 http://deb.debian.org/debian bullseye/main amd64 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 47 http://deb.debian.org/debian bullseye/main amd64 libelf1 amd64 0.183-1 [165 kB] Get: 48 http://deb.debian.org/debian bullseye/main amd64 dwz amd64 0.13+20210201-1 [175 kB] Get: 49 http://deb.debian.org/debian bullseye/main amd64 libicu67 amd64 67.1-7 [8622 kB] Get: 50 http://deb.debian.org/debian bullseye/main amd64 libxml2 amd64 2.9.10+dfsg-6.7+deb11u4 [693 kB] Get: 51 http://deb.debian.org/debian bullseye/main amd64 gettext amd64 0.21-4 [1311 kB] Get: 52 http://deb.debian.org/debian bullseye/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 53 http://deb.debian.org/debian bullseye/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 54 http://deb.debian.org/debian bullseye/main amd64 debhelper all 13.3.4 [1049 kB] Get: 55 http://deb.debian.org/debian bullseye/main amd64 python3-lib2to3 all 3.9.2-1 [77.8 kB] Get: 56 http://deb.debian.org/debian bullseye/main amd64 python3-distutils all 3.9.2-1 [143 kB] Get: 57 http://deb.debian.org/debian bullseye/main amd64 dh-python all 4.20201102+nmu1 [99.4 kB] Get: 58 http://deb.debian.org/debian bullseye/main amd64 xml-core all 0.18+nmu1 [23.8 kB] Get: 59 http://deb.debian.org/debian bullseye/main amd64 docutils-common all 0.16+dfsg-4 [129 kB] Get: 60 http://deb.debian.org/debian bullseye/main amd64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [517 kB] Get: 61 http://deb.debian.org/debian bullseye/main amd64 fonts-lyx all 2.3.6-1 [205 kB] Get: 62 http://deb.debian.org/debian bullseye/main amd64 fonts-mathjax all 2.7.9+dfsg-1 [2210 kB] Get: 63 http://deb.debian.org/debian bullseye/main amd64 libaec0 amd64 1.0.4-1 [20.3 kB] Get: 64 http://deb.debian.org/debian bullseye/main amd64 libblas3 amd64 3.9.0-3+deb11u1 [153 kB] Get: 65 http://deb.debian.org/debian bullseye/main amd64 libsnappy1v5 amd64 1.1.8-1 [17.9 kB] Get: 66 http://deb.debian.org/debian bullseye/main amd64 libblosc1 amd64 1.20.1+ds1-2 [48.7 kB] Get: 67 http://deb.debian.org/debian bullseye/main amd64 libbrotli1 amd64 1.0.9-2+b2 [279 kB] Get: 68 http://deb.debian.org/debian bullseye/main amd64 libmd0 amd64 1.0.3-3 [28.0 kB] Get: 69 http://deb.debian.org/debian bullseye/main amd64 libbsd0 amd64 0.11.3-1+deb11u1 [108 kB] Get: 70 http://deb.debian.org/debian bullseye/main amd64 libdeflate0 amd64 1.7-1 [53.1 kB] Get: 71 http://deb.debian.org/debian bullseye/main amd64 libexpat1-dev amd64 2.2.10-2+deb11u5 [141 kB] Get: 72 http://deb.debian.org/debian bullseye/main amd64 libpng16-16 amd64 1.6.37-3 [294 kB] Get: 73 http://deb.debian.org/debian bullseye/main amd64 libfreetype6 amd64 2.10.4+dfsg-1+deb11u1 [418 kB] Get: 74 http://deb.debian.org/debian bullseye/main amd64 libgfortran5 amd64 10.2.1-6 [727 kB] Get: 75 http://deb.debian.org/debian bullseye/main amd64 libsz2 amd64 1.0.4-1 [6760 B] Get: 76 http://deb.debian.org/debian bullseye/main amd64 libhdf5-103-1 amd64 1.10.6+repack-4+deb11u1 [1189 kB] Get: 77 http://deb.debian.org/debian bullseye/main amd64 libimagequant0 amd64 2.12.2-1.1 [32.5 kB] Get: 78 http://deb.debian.org/debian bullseye/main amd64 libjbig0 amd64 2.1-3.1+b2 [31.0 kB] Get: 79 http://deb.debian.org/debian bullseye/main amd64 libjpeg62-turbo amd64 1:2.0.6-4 [151 kB] Get: 80 http://deb.debian.org/debian bullseye/main amd64 libjs-jquery all 3.5.1+dfsg+~3.5.5-7 [315 kB] Get: 81 http://deb.debian.org/debian bullseye/main amd64 libjs-jquery-ui all 1.12.1+dfsg-8+deb11u1 [232 kB] Get: 82 http://deb.debian.org/debian bullseye/main amd64 libjs-mathjax all 2.7.9+dfsg-1 [5667 kB] Get: 83 http://deb.debian.org/debian bullseye/main amd64 libjs-underscore all 1.9.1~dfsg-3 [100 kB] Get: 84 http://deb.debian.org/debian bullseye/main amd64 libjs-sphinxdoc all 3.4.3-2 [127 kB] Get: 85 http://deb.debian.org/debian bullseye/main amd64 liblapack3 amd64 3.9.0-3+deb11u1 [2166 kB] Get: 86 http://deb.debian.org/debian bullseye/main amd64 liblbfgsb0 amd64 3.0+dfsg.3-9 [28.5 kB] Get: 87 http://deb.debian.org/debian bullseye/main amd64 liblcms2-2 amd64 2.12~rc1-2 [150 kB] Get: 88 http://deb.debian.org/debian bullseye/main amd64 liblzo2-2 amd64 2.10-2 [56.9 kB] Get: 89 http://deb.debian.org/debian bullseye/main amd64 libnorm1 amd64 1.5.9+dfsg-2 [221 kB] Get: 90 http://deb.debian.org/debian bullseye/main amd64 libpgm-5.3-0 amd64 5.3.128~dfsg-2 [161 kB] Get: 91 http://deb.debian.org/debian bullseye/main amd64 libpython3.9 amd64 3.9.2-1 [1691 kB] Get: 92 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-dev amd64 3.9.2-1 [4028 kB] Get: 93 http://deb.debian.org/debian bullseye/main amd64 libpython3-dev amd64 3.9.2-3 [21.7 kB] Get: 94 http://deb.debian.org/debian bullseye/main amd64 libpython3-all-dev amd64 3.9.2-3 [1068 B] Get: 95 http://deb.debian.org/debian bullseye/main amd64 libsodium23 amd64 1.0.18-1 [161 kB] Get: 96 http://deb.debian.org/debian bullseye/main amd64 libwebp6 amd64 0.6.1-2.1+deb11u2 [259 kB] Get: 97 http://deb.debian.org/debian bullseye/main amd64 libtiff5 amd64 4.2.0-1+deb11u4 [290 kB] Get: 98 http://deb.debian.org/debian bullseye/main amd64 libwebpdemux2 amd64 0.6.1-2.1+deb11u2 [87.8 kB] Get: 99 http://deb.debian.org/debian bullseye/main amd64 libwebpmux3 amd64 0.6.1-2.1+deb11u2 [97.7 kB] Get: 100 http://deb.debian.org/debian bullseye/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB] Get: 101 http://deb.debian.org/debian bullseye/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get: 102 http://deb.debian.org/debian bullseye/main amd64 libxcb1 amd64 1.14-3 [140 kB] Get: 103 http://deb.debian.org/debian bullseye/main amd64 libzmq5 amd64 4.3.4-1 [275 kB] Get: 104 http://deb.debian.org/debian bullseye/main amd64 python-babel-localedata all 2.8.0+dfsg.1-7 [4997 kB] Get: 105 http://deb.debian.org/debian bullseye/main amd64 ttf-bitstream-vera all 1.10-8.1 [223 kB] Get: 106 http://deb.debian.org/debian bullseye/main amd64 python-matplotlib-data all 3.3.4-1 [4153 kB] Get: 107 http://deb.debian.org/debian bullseye/main amd64 python-tables-data all 3.6.1-3 [53.1 kB] Get: 108 http://deb.debian.org/debian bullseye/main amd64 python3-alabaster all 0.7.8-1.1 [18.6 kB] Get: 109 http://deb.debian.org/debian bullseye/main amd64 python3-all amd64 3.9.2-3 [1056 B] Get: 110 http://deb.debian.org/debian bullseye/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-2+deb11u2 [191 kB] Get: 111 http://deb.debian.org/debian bullseye/main amd64 python3.9-dev amd64 3.9.2-1 [515 kB] Get: 112 http://deb.debian.org/debian bullseye/main amd64 python3-dev amd64 3.9.2-3 [24.8 kB] Get: 113 http://deb.debian.org/debian bullseye/main amd64 python3-all-dev amd64 3.9.2-3 [1064 B] Get: 114 http://deb.debian.org/debian bullseye/main amd64 python3-astor all 0.8.1-1 [23.2 kB] Get: 115 http://deb.debian.org/debian bullseye/main amd64 python3-attr all 20.3.0-1 [52.9 kB] Get: 116 http://deb.debian.org/debian bullseye/main amd64 python3-pkg-resources all 52.0.0-4 [190 kB] Get: 117 http://deb.debian.org/debian bullseye/main amd64 python3-tz all 2021.1-1 [34.8 kB] Get: 118 http://deb.debian.org/debian bullseye/main amd64 python3-babel all 2.8.0+dfsg.1-7 [100 kB] Get: 119 http://deb.debian.org/debian bullseye/main amd64 python3-backcall all 0.2.0-1 [10.7 kB] Get: 120 http://deb.debian.org/debian bullseye/main amd64 python3-pyparsing all 2.4.7-1 [109 kB] Get: 121 http://deb.debian.org/debian bullseye/main amd64 python3-packaging all 20.9-2 [33.5 kB] Get: 122 http://deb.debian.org/debian bullseye/main amd64 python3-six all 1.16.0-2 [17.5 kB] Get: 123 http://deb.debian.org/debian bullseye/main amd64 python3-webencodings all 0.5.1-2 [11.0 kB] Get: 124 http://deb.debian.org/debian bullseye/main amd64 python3-html5lib all 1.1-3 [93.0 kB] Get: 125 http://deb.debian.org/debian bullseye/main amd64 python3-bleach all 3.2.1-2.1 [36.5 kB] Get: 126 http://deb.debian.org/debian bullseye/main amd64 python3-certifi all 2020.6.20-1 [151 kB] Get: 127 http://deb.debian.org/debian bullseye/main amd64 python3-chardet all 4.0.0-1 [99.0 kB] Get: 128 http://deb.debian.org/debian bullseye/main amd64 python3-cycler all 0.10.0-3 [8084 B] Get: 129 http://deb.debian.org/debian bullseye/main amd64 python3-dateutil all 2.8.1-6 [79.2 kB] Get: 130 http://deb.debian.org/debian bullseye/main amd64 python3-decorator all 4.4.2-2 [15.8 kB] Get: 131 http://deb.debian.org/debian bullseye/main amd64 python3-defusedxml all 0.6.0-2 [38.2 kB] Get: 132 http://deb.debian.org/debian bullseye/main amd64 python3-roman all 2.0.0-5 [9064 B] Get: 133 http://deb.debian.org/debian bullseye/main amd64 python3-docutils all 0.16+dfsg-4 [384 kB] Get: 134 http://deb.debian.org/debian bullseye/main amd64 python3-entrypoints all 0.3-5 [5848 B] Get: 135 http://deb.debian.org/debian bullseye/main amd64 python3-idna all 2.10-1 [37.4 kB] Get: 136 http://deb.debian.org/debian bullseye/main amd64 python3-imagesize all 1.2.0-2 [5824 B] Get: 137 http://deb.debian.org/debian bullseye/main amd64 python3-more-itertools all 4.2.0-3 [42.7 kB] Get: 138 http://deb.debian.org/debian bullseye/main amd64 python3-zipp all 1.0.0-3 [6060 B] Get: 139 http://deb.debian.org/debian bullseye/main amd64 python3-importlib-metadata all 1.6.0-2 [10.3 kB] Get: 140 http://deb.debian.org/debian bullseye/main amd64 python3-parso all 0.8.1-1 [65.9 kB] Get: 141 http://deb.debian.org/debian bullseye/main amd64 python3-jedi all 0.18.0-1 [620 kB] Get: 142 http://deb.debian.org/debian bullseye/main amd64 python3-ptyprocess all 0.7.0-1 [13.6 kB] Get: 143 http://deb.debian.org/debian bullseye/main amd64 python3-pexpect all 4.8.0-2 [54.9 kB] Get: 144 http://deb.debian.org/debian bullseye/main amd64 python3-pickleshare all 0.7.5-3 [7604 B] Get: 145 http://deb.debian.org/debian bullseye/main amd64 python3-wcwidth all 0.1.9+dfsg1-2 [18.2 kB] Get: 146 http://deb.debian.org/debian bullseye/main amd64 python3-prompt-toolkit all 3.0.14-1 [258 kB] Get: 147 http://deb.debian.org/debian bullseye/main amd64 python3-pygments all 2.7.1+dfsg-2.1 [657 kB] Get: 148 http://deb.debian.org/debian bullseye/main amd64 python3-ipython-genutils all 0.2.0-4 [21.4 kB] Get: 149 http://deb.debian.org/debian bullseye/main amd64 python3-traitlets all 5.0.5-1 [84.4 kB] Get: 150 http://deb.debian.org/debian bullseye/main amd64 python3-ipython all 7.20.0-1+deb11u1 [517 kB] Get: 151 http://deb.debian.org/debian bullseye/main amd64 python3-jupyter-core all 4.7.1-1+deb11u1 [44.2 kB] Get: 152 http://deb.debian.org/debian bullseye/main amd64 python3-tornado amd64 6.1.0-1+b1 [338 kB] Get: 153 http://deb.debian.org/debian bullseye/main amd64 python3-zmq amd64 20.0.0-1+b1 [262 kB] Get: 154 http://deb.debian.org/debian bullseye/main amd64 python3-jupyter-client all 6.1.11-2 [76.6 kB] Get: 155 http://deb.debian.org/debian bullseye/main amd64 python3-ipykernel all 5.4.3-1 [84.9 kB] Get: 156 http://deb.debian.org/debian bullseye/main amd64 python3-markupsafe amd64 1.1.1-1+b3 [15.2 kB] Get: 157 http://deb.debian.org/debian bullseye/main amd64 python3-jinja2 all 2.11.3-1 [114 kB] Get: 158 http://deb.debian.org/debian bullseye/main amd64 python3-joblib all 0.17.0-4+deb11u1 [214 kB] Get: 159 http://deb.debian.org/debian bullseye/main amd64 python3-setuptools all 52.0.0-4 [366 kB] Get: 160 http://deb.debian.org/debian bullseye/main amd64 python3-pyrsistent amd64 0.15.5-1+b3 [59.1 kB] Get: 161 http://deb.debian.org/debian bullseye/main amd64 python3-jsonschema all 3.2.0-3 [46.3 kB] Get: 162 http://deb.debian.org/debian bullseye/main amd64 python3-kiwisolver amd64 1.3.1-1+b1 [55.7 kB] Get: 163 http://deb.debian.org/debian bullseye/main amd64 python3-numpy amd64 1:1.19.5-1 [2693 kB] Get: 164 http://deb.debian.org/debian bullseye/main amd64 python3-pil amd64 8.1.2+dfsg-0.3+deb11u1 [445 kB] Get: 165 http://deb.debian.org/debian bullseye/main amd64 python3-matplotlib amd64 3.3.4-1 [4163 kB] Get: 166 http://deb.debian.org/debian bullseye/main amd64 python3-mistune all 0.8.4-4 [16.4 kB] Get: 167 http://deb.debian.org/debian bullseye/main amd64 sphinx-rtd-theme-common all 0.5.1+dfsg-1 [995 kB] Get: 168 http://deb.debian.org/debian bullseye/main amd64 sphinx-common all 3.4.3-2 [578 kB] Get: 169 http://deb.debian.org/debian bullseye/main amd64 python3-urllib3 all 1.26.5-1~exp1 [114 kB] Get: 170 http://deb.debian.org/debian bullseye/main amd64 python3-requests all 2.25.1+dfsg-2 [69.3 kB] Get: 171 http://deb.debian.org/debian bullseye/main amd64 python3-snowballstemmer all 2.1.0-1 [58.7 kB] Get: 172 http://deb.debian.org/debian bullseye/main amd64 python3-sphinx all 3.4.3-2 [545 kB] Get: 173 http://deb.debian.org/debian bullseye/main amd64 python3-sphinx-rtd-theme all 0.5.1+dfsg-1 [20.9 kB] Get: 174 http://deb.debian.org/debian bullseye/main amd64 python3-msmb-theme all 1.2.0-2 [33.5 kB] Get: 175 http://deb.debian.org/debian bullseye/main amd64 python3-nbformat all 5.1.2-1 [51.6 kB] Get: 176 http://deb.debian.org/debian bullseye/main amd64 python3-pandocfilters all 1.4.3-1 [20.0 kB] Get: 177 http://deb.debian.org/debian bullseye/main amd64 python3-testpath all 0.4.4+dfsg-1 [8996 B] Get: 178 http://deb.debian.org/debian bullseye/main amd64 python3-nbconvert all 5.6.1-3 [356 kB] Get: 179 http://deb.debian.org/debian bullseye/main amd64 python3-networkx all 2.5+ds-2 [900 kB] Get: 180 http://deb.debian.org/debian bullseye/main amd64 python3-numexpr amd64 2.7.2-2 [144 kB] Get: 181 http://deb.debian.org/debian bullseye/main amd64 python3-numpydoc all 1.1.0-3 [40.0 kB] Get: 182 http://deb.debian.org/debian bullseye/main amd64 python3-pandas-lib amd64 1.1.5+dfsg-2 [3287 kB] Get: 183 http://deb.debian.org/debian bullseye/main amd64 python3-pandas all 1.1.5+dfsg-2 [2096 kB] Get: 184 http://deb.debian.org/debian bullseye/main amd64 python3-scipy amd64 1.6.0-2 [12.3 MB] Get: 185 http://deb.debian.org/debian bullseye/main amd64 python3-sklearn-lib amd64 0.23.2-5 [1884 kB] Get: 186 http://deb.debian.org/debian bullseye/main amd64 python3-threadpoolctl all 2.1.0-1 [15.3 kB] Get: 187 http://deb.debian.org/debian bullseye/main amd64 python3-sklearn all 0.23.2-5 [1818 kB] Get: 188 http://deb.debian.org/debian bullseye/main amd64 python3-tables-lib amd64 3.6.1-3 [394 kB] Get: 189 http://deb.debian.org/debian bullseye/main amd64 python3-tables all 3.6.1-3 [342 kB] Fetched 102 MB in 14s (7097 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 17743 files and directories currently installed.) Preparing to unpack .../0-bsdextrautils_2.36.1-8+deb11u1_amd64.deb ... Unpacking bsdextrautils (2.36.1-8+deb11u1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../1-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. 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Setting up libsodium23:amd64 (1.0.18-1) ... Setting up bsdextrautils (2.36.1-8+deb11u1) ... update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode Setting up libjs-mathjax (2.7.9+dfsg-1) ... Setting up libicu67:amd64 (67.1-7) ... Setting up libmagic-mgc (1:5.39-3+deb11u1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libpgm-5.3-0:amd64 (5.3.128~dfsg-2) ... Setting up fonts-lyx (2.3.6-1) ... Setting up libdebhelper-perl (13.3.4) ... Setting up libbrotli1:amd64 (1.0.9-2+b2) ... Setting up libnorm1:amd64 (1.5.9+dfsg-2) ... Setting up libmagic1:amd64 (1:5.39-3+deb11u1) ... Setting up libdeflate0:amd64 (1.7-1) ... Setting up gettext-base (0.21-4) ... Setting up liblzo2-2:amd64 (2.10-2) ... Setting up file (1:5.39-3+deb11u1) ... Setting up libjbig0:amd64 (2.1-3.1+b2) ... Setting up libaec0:amd64 (1.0.4-1) ... Setting up python-babel-localedata (2.8.0+dfsg.1-7) ... Setting up libsnappy1v5:amd64 (1.1.8-1) ... Setting up tzdata (2021a-1+deb11u10) ... Current default time zone: 'Etc/UTC' Local time is now: Sat Jan 6 12:32:23 UTC 2024. Universal Time is now: Sat Jan 6 12:32:23 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20180224.1+nmu1) ... Setting up libblas3:amd64 (3.9.0-3+deb11u1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libexpat1-dev:amd64 (2.2.10-2+deb11u5) ... Setting up libjpeg62-turbo:amd64 (1:2.0.6-4) ... Setting up libncurses6:amd64 (6.2+20201114-2+deb11u2) ... Setting up libsigsegv2:amd64 (2.13-1) ... Setting up libimagequant0:amd64 (2.12.2-1.1) ... Setting up libpng16-16:amd64 (1.6.37-3) ... Setting up autopoint (0.21-4) ... Setting up libwebp6:amd64 (0.6.1-2.1+deb11u2) ... Setting up libgfortran5:amd64 (10.2.1-6) ... Setting up zlib1g-dev:amd64 (1:1.2.11.dfsg-2+deb11u2) ... Setting up libmd0:amd64 (1.0.3-3) ... Setting up sensible-utils (0.0.14) ... Setting up libuchardet0:amd64 (0.0.7-1) ... Setting up libblosc1 (1.20.1+ds1-2) ... Setting up libmpdec3:amd64 (2.5.1-1) ... Setting up libsub-override-perl (0.09-2) ... Setting up sgml-base (1.30) ... Setting up libtiff5:amd64 (4.2.0-1+deb11u4) ... Setting up libjs-jquery (3.5.1+dfsg+~3.5.5-7) ... Setting up python-matplotlib-data (3.3.4-1) ... Setting up openssl (1.1.1w-0+deb11u1) ... Setting up libwebpmux3:amd64 (0.6.1-2.1+deb11u2) ... Setting up libbsd0:amd64 (0.11.3-1+deb11u1) ... Setting up mailcap (3.69) ... Setting up libelf1:amd64 (0.183-1) ... Setting up readline-common (8.1-1) ... Setting up libxml2:amd64 (2.9.10+dfsg-6.7+deb11u4) ... Setting up python-tables-data (3.6.1-3) ... Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... Setting up sphinx-rtd-theme-common (0.5.1+dfsg-1) ... Setting up libprocps8:amd64 (2:3.3.17-5) ... Setting up libsz2:amd64 (1.0.4-1) ... Setting up libjs-underscore (1.9.1~dfsg-3) ... Setting up libfile-stripnondeterminism-perl (1.12.0-1) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up liblapack3:amd64 (3.9.0-3+deb11u1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up libxcb1:amd64 (1.14-3) ... Setting up gettext (0.21-4) ... Setting up libzmq5:amd64 (4.3.4-1) ... Setting up mime-support (3.66) ... Setting up libtool (2.4.6-15) ... Setting up libwebpdemux2:amd64 (0.6.1-2.1+deb11u2) ... Setting up libreadline8:amd64 (8.1-1) ... Setting up m4 (1.4.18-5) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up ca-certificates (20210119) ... Updating certificates in /etc/ssl/certs... 129 added, 0 removed; done. Setting up libjs-jquery-ui (1.12.1+dfsg-8+deb11u1) ... Setting up libfreetype6:amd64 (2.10.4+dfsg-1+deb11u1) ... Setting up libjs-sphinxdoc (3.4.3-2) ... Setting up autoconf (2.69-14) ... Setting up dh-strip-nondeterminism (1.12.0-1) ... Setting up libhdf5-103-1:amd64 (1.10.6+repack-4+deb11u1) ... Setting up dwz (0.13+20210201-1) ... Setting up groff-base (1.22.4-6) ... Setting up xml-core (0.18+nmu1) ... Setting up procps (2:3.3.17-5) ... Setting up libpython3.9-stdlib:amd64 (3.9.2-1) ... Setting up libpython3-stdlib:amd64 (3.9.2-3) ... Setting up liblbfgsb0:amd64 (3.0+dfsg.3-9) ... Setting up automake (1:1.16.3-2) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up dh-autoreconf (20) ... Setting up libpython3.9:amd64 (3.9.2-1) ... Setting up sphinx-common (3.4.3-2) ... Setting up python3.9 (3.9.2-1) ... Setting up libpython3.9-dev:amd64 (3.9.2-1) ... Setting up debhelper (13.3.4) ... Setting up python3 (3.9.2-3) ... Setting up python3-pandocfilters (1.4.3-1) ... Setting up python3-markupsafe (1.1.1-1+b3) ... Setting up python3-webencodings (0.5.1-2) ... Setting up python3-tz (2021.1-1) ... Setting up python3-six (1.16.0-2) ... Setting up python3-pil:amd64 (8.1.2+dfsg-0.3+deb11u1) ... Setting up python3-roman (2.0.0-5) ... Setting up python3-decorator (4.4.2-2) ... Setting up python3-jinja2 (2.11.3-1) ... Setting up python3-wcwidth (0.1.9+dfsg1-2) ... Setting up python3-pyparsing (2.4.7-1) ... Setting up python3-certifi (2020.6.20-1) ... Setting up python3-snowballstemmer (2.1.0-1) ... Setting up python3-testpath (0.4.4+dfsg-1) ... Setting up python3-zmq (20.0.0-1+b1) ... Setting up python3-cycler (0.10.0-3) ... Setting up python3-kiwisolver (1.3.1-1+b1) ... Setting up python3-idna (2.10-1) ... Setting up cython3 (0.29.21-3+b1) ... Setting up python3-html5lib (1.1-3) ... Setting up python3-pickleshare (0.7.5-3) ... Setting up python3-urllib3 (1.26.5-1~exp1) ... Setting up python3-pyrsistent:amd64 (0.15.5-1+b3) ... Setting up python3.9-dev (3.9.2-1) ... Setting up python3-dateutil (2.8.1-6) ... Setting up python3-lib2to3 (3.9.2-1) ... Setting up python3-mistune (0.8.4-4) ... Setting up python3-astor (0.8.1-1) ... Setting up python3-imagesize (1.2.0-2) ... Setting up python3-ptyprocess (0.7.0-1) ... Setting up python3-pkg-resources (52.0.0-4) ... Setting up python3-entrypoints (0.3-5) ... Setting up python3-prompt-toolkit (3.0.14-1) ... Setting up python3-distutils (3.9.2-1) ... Setting up dh-python (4.20201102+nmu1) ... Setting up python3-more-itertools (4.2.0-3) ... Setting up python3-attr (20.3.0-1) ... Setting up python3-tornado (6.1.0-1+b1) ... Setting up libpython3-dev:amd64 (3.9.2-3) ... Setting up python3-setuptools (52.0.0-4) ... Setting up python3-backcall (0.2.0-1) ... Setting up python3-joblib (0.17.0-4+deb11u1) ... Setting up python3-parso (0.8.1-1) ... Setting up python3-babel (2.8.0+dfsg.1-7) ... update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up python3-defusedxml (0.6.0-2) ... Setting up python3-ipython-genutils (0.2.0-4) ... Setting up python3-alabaster (0.7.8-1.1) ... Setting up python3-threadpoolctl (2.1.0-1) ... Setting up python3-all (3.9.2-3) ... Setting up python3-zipp (1.0.0-3) ... Setting up python3-networkx (2.5+ds-2) ... Setting up python3-pygments (2.7.1+dfsg-2.1) ... Setting up python3-packaging (20.9-2) ... Setting up python3-chardet (4.0.0-1) ... Setting up libpython3-all-dev:amd64 (3.9.2-3) ... Setting up python3-pexpect (4.8.0-2) ... Setting up python3-dev (3.9.2-3) ... Setting up python3-requests (2.25.1+dfsg-2) ... Setting up python3-numpy (1:1.19.5-1) ... Setting up python3-traitlets (5.0.5-1) ... Setting up python3-jupyter-core (4.7.1-1+deb11u1) ... Setting up python3-all-dev (3.9.2-3) ... Setting up python3-matplotlib (3.3.4-1) ... Setting up python3-scipy (1.6.0-2) ... Setting up python3-importlib-metadata (1.6.0-2) ... Setting up python3-jedi (0.18.0-1) ... Setting up python3-tables-lib (3.6.1-3) ... Setting up python3-pandas-lib:amd64 (1.1.5+dfsg-2) ... Setting up python3-sklearn-lib:amd64 (0.23.2-5) ... Setting up python3-bleach (3.2.1-2.1) ... Setting up python3-pandas (1.1.5+dfsg-2) ... Setting up python3-jsonschema (3.2.0-3) ... Setting up python3-ipython (7.20.0-1+deb11u1) ... Setting up python3-sklearn (0.23.2-5) ... Setting up python3-numexpr (2.7.2-2) ... Setting up python3-jupyter-client (6.1.11-2) ... Setting up python3-nbformat (5.1.2-1) ... Setting up python3-tables (3.6.1-3) ... Setting up python3-ipykernel (5.4.3-1) ... Setting up python3-nbconvert (5.6.1-3) ... Processing triggers for libc-bin (2.31-13+deb11u6) ... Processing triggers for sgml-base (1.30) ... Setting up docutils-common (0.16+dfsg-4) ... Processing triggers for sgml-base (1.30) ... Setting up python3-docutils (0.16+dfsg-4) ... update-alternatives: using /usr/share/docutils/scripts/python3/rst-buildhtml to provide /usr/bin/rst-buildhtml (rst-buildhtml) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2html to provide /usr/bin/rst2html (rst2html) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2html4 to provide /usr/bin/rst2html4 (rst2html4) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2html5 to provide /usr/bin/rst2html5 (rst2html5) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2latex to provide /usr/bin/rst2latex (rst2latex) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2man to provide /usr/bin/rst2man (rst2man) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2odt to provide /usr/bin/rst2odt (rst2odt) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2odt_prepstyles to provide /usr/bin/rst2odt_prepstyles (rst2odt_prepstyles) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2pseudoxml to provide /usr/bin/rst2pseudoxml (rst2pseudoxml) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2s5 to provide /usr/bin/rst2s5 (rst2s5) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2xetex to provide /usr/bin/rst2xetex (rst2xetex) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2xml to provide /usr/bin/rst2xml (rst2xml) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rstpep2html to provide /usr/bin/rstpep2html (rstpep2html) in auto mode Setting up python3-sphinx (3.4.3-2) ... Setting up python3-sphinx-rtd-theme (0.5.1+dfsg-1) ... Setting up python3-numpydoc (1.1.0-3) ... Setting up python3-msmb-theme (1.2.0-2) ... Processing triggers for ca-certificates (20210119) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.25.3-1.1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: user script /srv/workspace/pbuilder/4100091/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for bullseye I: user script /srv/workspace/pbuilder/4100091/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/mdtraj-1.9.5/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../mdtraj_1.9.5-1_source.changes dpkg-buildpackage: info: source package mdtraj dpkg-buildpackage: info: source version 1.9.5-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Drew Parsons dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 dpkg-source: info: using options from mdtraj-1.9.5/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/ fakeroot debian/rules clean dh clean --with python3,sphinxdoc --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/mdtraj-1.9.5' dh_auto_clean || /bin/true I: pybuild base:232: python3.9 setup.py clean Using built-in specs. COLLECT_GCC=/usr/bin/x86_64-linux-gnu-gcc COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/10/lto-wrapper OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa:hsa OFFLOAD_TARGET_DEFAULT=1 Target: x86_64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 10.2.1-6' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/gcc-10-Km9U7s/gcc-10-10.2.1/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-10-Km9U7s/gcc-10-10.2.1/debian/tmp-gcn/usr,hsa --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-mutex Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 10.2.1 20210110 (Debian 10.2.1-6) ./basesetup.py:431: UserWarning: Unrecognized setuptools command ('clean'), proceeding with generating Cython sources and expanding templates warnings.warn("Unrecognized setuptools command ('{}'), proceeding with " warning: mdtraj/formats/dcd/dcdlib.pxd:12:12: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. warning: mdtraj/formats/dcd/dcdlib.pxd:12:16: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. warning: mdtraj/formats/dcd/dcdlib.pxd:12:20: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. C compiler: Attempting to autodetect OpenMP support... Compiler supports OpenMP Attempting to autodetect SSE3 support... Compiler supports SSE3 Attempting to autodetect SSE4.1 support... Compiler supports SSE4.1 Attempting to autodetect NEON support... Did not detect NEON support Compiling mdtraj/formats/xtc/xtc.pyx because it changed. Compiling mdtraj/formats/xtc/trr.pyx because it changed. Compiling mdtraj/formats/tng/tng.pyx because it changed. Compiling mdtraj/formats/dcd/dcd.pyx because it changed. Compiling mdtraj/formats/binpos/binpos.pyx because it changed. Compiling mdtraj/formats/dtr/dtr.pyx because it changed. Compiling mdtraj/rmsd/_rmsd.pyx because it changed. Compiling mdtraj/rmsd/_lprmsd.pyx because it changed. Compiling mdtraj/geometry/src/_geometry.pyx because it changed. Compiling mdtraj/geometry/drid.pyx because it changed. Compiling mdtraj/geometry/neighbors.pyx because it changed. Compiling mdtraj/geometry/neighborlist.pyx because it changed. [ 1/12] Cythonizing mdtraj/formats/binpos/binpos.pyx [ 2/12] Cythonizing mdtraj/formats/dcd/dcd.pyx [ 3/12] Cythonizing mdtraj/formats/dtr/dtr.pyx [ 4/12] Cythonizing mdtraj/formats/tng/tng.pyx [ 5/12] Cythonizing mdtraj/formats/xtc/trr.pyx [ 6/12] Cythonizing mdtraj/formats/xtc/xtc.pyx [ 7/12] Cythonizing mdtraj/geometry/drid.pyx [ 8/12] Cythonizing mdtraj/geometry/neighborlist.pyx [ 9/12] Cythonizing mdtraj/geometry/neighbors.pyx [10/12] Cythonizing mdtraj/geometry/src/_geometry.pyx [11/12] Cythonizing mdtraj/rmsd/_lprmsd.pyx [12/12] Cythonizing mdtraj/rmsd/_rmsd.pyx running clean removing '/build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build' (and everything under it) 'build/bdist.linux-x86_64' does not exist -- can't clean it 'build/scripts-3.9' does not exist -- can't clean it for f in mdtraj/formats/binpos/binpos.c \ mdtraj/formats/dcd/dcd.c \ mdtraj/formats/dtr/dtr.cpp \ mdtraj/formats/tng/tng.c \ mdtraj/formats/xtc/trr.c \ mdtraj/formats/xtc/xtc.c \ mdtraj/geometry/drid.cpp \ mdtraj/geometry/neighborlist.cpp \ mdtraj/geometry/neighbors.cpp \ mdtraj/geometry/src/_geometry.cpp \ mdtraj/rmsd/_lprmsd.cpp \ mdtraj/rmsd/_rmsd.cpp \ mdtraj/version.py; \ do rm -f $f; done rm -rf __pycache__ make[1]: Leaving directory '/build/reproducible-path/mdtraj-1.9.5' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules build dh build --with python3,sphinxdoc --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:232: python3.9 setup.py config Using built-in specs. COLLECT_GCC=/usr/bin/x86_64-linux-gnu-gcc COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/10/lto-wrapper OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa:hsa OFFLOAD_TARGET_DEFAULT=1 Target: x86_64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 10.2.1-6' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/gcc-10-Km9U7s/gcc-10-10.2.1/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-10-Km9U7s/gcc-10-10.2.1/debian/tmp-gcn/usr,hsa --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-mutex Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 10.2.1 20210110 (Debian 10.2.1-6) ./basesetup.py:431: UserWarning: Unrecognized setuptools command ('config'), proceeding with generating Cython sources and expanding templates warnings.warn("Unrecognized setuptools command ('{}'), proceeding with " warning: mdtraj/formats/dcd/dcdlib.pxd:12:12: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. warning: mdtraj/formats/dcd/dcdlib.pxd:12:16: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. warning: mdtraj/formats/dcd/dcdlib.pxd:12:20: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. C compiler: Attempting to autodetect OpenMP support... Compiler supports OpenMP Attempting to autodetect SSE3 support... Compiler supports SSE3 Attempting to autodetect SSE4.1 support... Compiler supports SSE4.1 Attempting to autodetect NEON support... Did not detect NEON support Compiling mdtraj/formats/xtc/xtc.pyx because it changed. Compiling mdtraj/formats/xtc/trr.pyx because it changed. Compiling mdtraj/formats/tng/tng.pyx because it changed. Compiling mdtraj/formats/dcd/dcd.pyx because it changed. Compiling mdtraj/formats/binpos/binpos.pyx because it changed. Compiling mdtraj/formats/dtr/dtr.pyx because it changed. Compiling mdtraj/rmsd/_rmsd.pyx because it changed. Compiling mdtraj/rmsd/_lprmsd.pyx because it changed. Compiling mdtraj/geometry/src/_geometry.pyx because it changed. Compiling mdtraj/geometry/drid.pyx because it changed. Compiling mdtraj/geometry/neighbors.pyx because it changed. Compiling mdtraj/geometry/neighborlist.pyx because it changed. [ 1/12] Cythonizing mdtraj/formats/binpos/binpos.pyx [ 2/12] Cythonizing mdtraj/formats/dcd/dcd.pyx [ 3/12] Cythonizing mdtraj/formats/dtr/dtr.pyx [ 4/12] Cythonizing mdtraj/formats/tng/tng.pyx [ 5/12] Cythonizing mdtraj/formats/xtc/trr.pyx [ 6/12] Cythonizing mdtraj/formats/xtc/xtc.pyx [ 7/12] Cythonizing mdtraj/geometry/drid.pyx [ 8/12] Cythonizing mdtraj/geometry/neighborlist.pyx [ 9/12] Cythonizing mdtraj/geometry/neighbors.pyx [10/12] Cythonizing mdtraj/geometry/src/_geometry.pyx [11/12] Cythonizing mdtraj/rmsd/_lprmsd.pyx [12/12] Cythonizing mdtraj/rmsd/_rmsd.pyx running config debian/rules override_dh_auto_build-indep make[1]: Entering directory '/build/reproducible-path/mdtraj-1.9.5' dh_auto_build I: pybuild base:232: /usr/bin/python3 setup.py build Using built-in specs. COLLECT_GCC=/usr/bin/x86_64-linux-gnu-gcc COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/10/lto-wrapper OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa:hsa OFFLOAD_TARGET_DEFAULT=1 Target: x86_64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 10.2.1-6' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/gcc-10-Km9U7s/gcc-10-10.2.1/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-10-Km9U7s/gcc-10-10.2.1/debian/tmp-gcn/usr,hsa --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-mutex Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 10.2.1 20210110 (Debian 10.2.1-6) C compiler: Attempting to autodetect OpenMP support... Compiler supports OpenMP Attempting to autodetect SSE3 support... Compiler supports SSE3 Attempting to autodetect SSE4.1 support... Compiler supports SSE4.1 Attempting to autodetect NEON support... Did not detect NEON support running build running build_py creating /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj copying mdtraj/version.py -> /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj copying mdtraj/io.py -> /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj copying mdtraj/__init__.py -> /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj creating /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils copying mdtraj/utils/zipped.py -> /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils copying mdtraj/utils/validation.py -> /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils copying mdtraj/utils/unitcell.py -> /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils copying mdtraj/utils/six.py -> /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils copying mdtraj/utils/singleton.py -> /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils copying mdtraj/utils/rotation.py -> /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils copying mdtraj/utils/delay_import.py -> /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils copying mdtraj/utils/contextmanagers.py -> /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils copying mdtraj/utils/__init__.py -> /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils creating /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/testing copying mdtraj/testing/testing.py -> /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/testing copying mdtraj/testing/docstrings.py -> /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/testing copying mdtraj/testing/docscrape.py -> /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/testing copying mdtraj/testing/__init__.py -> /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/testing creating /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/scripts copying mdtraj/scripts/mdinspect.py -> /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/scripts copying mdtraj/scripts/mdconvert.py -> /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/scripts copying mdtraj/scripts/__init__.py -> /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/scripts creating /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/xtcreporter.py -> /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/netcdfreporter.py -> /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/hdf5reporter.py -> /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/dcdreporter.py -> /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/basereporter.py -> /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/__init__.py -> /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/reporters creating /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/nmr copying mdtraj/nmr/shift_wrappers.py -> /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/nmr copying mdtraj/nmr/scalar_couplings.py -> /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/nmr copying mdtraj/nmr/__init__.py -> /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/nmr creating /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/thermodynamic_properties.py -> /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/shape.py -> /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/sasa.py -> /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/rg.py -> /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/rdf.py -> /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/order.py -> /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/internal.py -> /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/hbond.py -> /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/dssp.py -> /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/distance.py -> /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/dihedral.py -> /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/contact.py -> /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/angle.py -> /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/alignment.py -> /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/__init__.py -> /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry creating /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats copying mdtraj/formats/xyzfile.py -> /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats copying mdtraj/formats/registry.py -> /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats copying mdtraj/formats/psf.py -> /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats copying mdtraj/formats/prmtop.py -> /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats copying mdtraj/formats/openmmxml.py -> /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats copying mdtraj/formats/netcdf.py -> /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats copying mdtraj/formats/mol2.py -> /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats copying mdtraj/formats/mdcrd.py -> /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats copying mdtraj/formats/lh5.py -> /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats copying mdtraj/formats/lammpstrj.py -> /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats copying mdtraj/formats/hoomdxml.py -> /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats copying mdtraj/formats/hdf5.py -> /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats copying mdtraj/formats/gsd.py -> /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats copying mdtraj/formats/gro.py -> /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats copying mdtraj/formats/arc.py -> /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats copying mdtraj/formats/amberrst.py -> /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats copying mdtraj/formats/__init__.py -> /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats creating /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/core copying mdtraj/core/selection.py -> /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/core copying mdtraj/core/trajectory.py -> /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/core copying mdtraj/core/topology.py -> /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/core copying mdtraj/core/residue_names.py -> /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/core copying mdtraj/core/element.py -> /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/core copying mdtraj/core/__init__.py -> /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/core creating /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/unit_operators.py -> /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/unit_math.py -> /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/unit_definitions.py -> /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/standard_dimensions.py -> /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/quantity.py -> /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/prefix.py -> /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/constants.py -> /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/unit.py -> /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/mymatrix.py -> /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/doctests.py -> /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/baseunit.py -> /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/basedimension.py -> /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/__init__.py -> /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit creating /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/pdb copying mdtraj/formats/pdb/pdbstructure.py -> /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/pdb copying mdtraj/formats/pdb/pdbfile.py -> /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/pdb copying mdtraj/formats/pdb/__init__.py -> /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/pdb creating /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/pdb/data copying mdtraj/formats/pdb/data/residues.xml -> /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/pdb/data copying mdtraj/formats/pdb/data/pdbNames.xml -> /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/pdb/data running build_ext building 'mdtraj.formats.xtc' extension creating build creating build/temp.linux-x86_64-3.9 creating build/temp.linux-x86_64-3.9/mdtraj creating build/temp.linux-x86_64-3.9/mdtraj/formats creating build/temp.linux-x86_64-3.9/mdtraj/formats/xtc creating build/temp.linux-x86_64-3.9/mdtraj/formats/xtc/src x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/xtc/src/xdrfile.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_decompress_coord_float': mdtraj/formats/xtc/src/xdrfile.c:788:25: warning: variable 'larger' set but not used [-Wunused-but-set-variable] 788 | int smallnum, smaller, larger, i, is_smaller, run; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c:785:16: warning: variable 'minidx' set but not used [-Wunused-but-set-variable] 785 | int smallidx, minidx, maxidx; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_compress_coord_float': mdtraj/formats/xtc/src/xdrfile.c:1016:6: warning: variable 'errval' set but not used [-Wunused-but-set-variable] 1016 | int errval=1; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_decompress_coord_double': mdtraj/formats/xtc/src/xdrfile.c:1305:25: warning: variable 'larger' set but not used [-Wunused-but-set-variable] 1305 | int smallnum, smaller, larger, i, is_smaller, run; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c:1302:16: warning: variable 'minidx' set but not used [-Wunused-but-set-variable] 1302 | int smallidx, minidx, maxidx; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_compress_coord_double': mdtraj/formats/xtc/src/xdrfile.c:1509:6: warning: variable 'errval' set but not used [-Wunused-but-set-variable] 1509 | int errval=1; | ^~~~~~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/xtc/src/xdrfile_xtc.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/xtc/src/xdrfile_xtc.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/formats/xtc/src/xdrfile_xtc.c: In function 'xtc_coord': mdtraj/formats/xtc/src/xdrfile_xtc.c:66:8: warning: unused variable 'j' [-Wunused-variable] 66 | int i,j,result; | ^ mdtraj/formats/xtc/src/xdrfile_xtc.c:66:6: warning: unused variable 'i' [-Wunused-variable] 66 | int i,j,result; | ^ mdtraj/formats/xtc/src/xdrfile_xtc.c: In function 'read_xtc_nframes': mdtraj/formats/xtc/src/xdrfile_xtc.c:119:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 119 | if (NULL == xd) | ^~ mdtraj/formats/xtc/src/xdrfile_xtc.c:122:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 122 | do { | ^~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/xtc/xtc.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/xtc/xtc.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1822, 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:4, from mdtraj/formats/xtc/xtc.c:639: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ mdtraj/formats/xtc/xtc.c: In function '__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_16_write': mdtraj/formats/xtc/xtc.c:553:40: warning: '__pyx_v_status' may be used uninitialized in this function [-Wmaybe-uninitialized] 553 | #define PyInt_FromLong PyLong_FromLong | ^~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:9374:7: note: '__pyx_v_status' was declared here 9374 | int __pyx_v_status; | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c: In function '__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_12_read': mdtraj/formats/xtc/xtc.c:7893:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[2].shape' may be used uninitialized in this function [-Wmaybe-uninitialized] 7893 | } else if (unlikely(__pyx_t_39 >= __pyx_pybuffernd_xyz_stride.diminfo[2].shape)) __pyx_t_6 = 2; | ^ mdtraj/formats/xtc/xtc.c:7889:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[1].shape' may be used uninitialized in this function [-Wmaybe-uninitialized] 7889 | } else if (unlikely(__pyx_t_38 >= __pyx_pybuffernd_xyz_stride.diminfo[1].shape)) __pyx_t_6 = 1; | ^ mdtraj/formats/xtc/xtc.c:7885:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[0].shape' may be used uninitialized in this function [-Wmaybe-uninitialized] 7885 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_xyz_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:7845:23: warning: '__pyx_pybuffernd_time_stride.diminfo[0].shape' may be used uninitialized in this function [-Wmaybe-uninitialized] 7845 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_time_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:7827:23: warning: '__pyx_pybuffernd_step_stride.diminfo[0].shape' may be used uninitialized in this function [-Wmaybe-uninitialized] 7827 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_step_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:7903:23: warning: '__pyx_pybuffernd_prec_stride.diminfo[0].shape' may be used uninitialized in this function [-Wmaybe-uninitialized] 7903 | } else if (unlikely(__pyx_t_40 >= __pyx_pybuffernd_prec_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:7865:23: warning: '__pyx_pybuffernd_box_stride.diminfo[2].shape' may be used uninitialized in this function [-Wmaybe-uninitialized] 7865 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_box_stride.diminfo[2].shape)) __pyx_t_6 = 2; | ^ mdtraj/formats/xtc/xtc.c:7861:23: warning: '__pyx_pybuffernd_box_stride.diminfo[1].shape' may be used uninitialized in this function [-Wmaybe-uninitialized] 7861 | } else if (unlikely(__pyx_t_33 >= __pyx_pybuffernd_box_stride.diminfo[1].shape)) __pyx_t_6 = 1; | ^ mdtraj/formats/xtc/xtc.c:7857:23: warning: '__pyx_pybuffernd_box_stride.diminfo[0].shape' may be used uninitialized in this function [-Wmaybe-uninitialized] 7857 | } else if (unlikely(__pyx_t_32 >= __pyx_pybuffernd_box_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:7480:17: warning: '__pyx_pybuffernd_framebuffer.diminfo[1].shape' may be used uninitialized in this function [-Wmaybe-uninitialized] 7480 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_framebuffer.diminfo[1].shape)) __pyx_t_6 = 1; | ^ mdtraj/formats/xtc/xtc.c:7476:17: warning: '__pyx_pybuffernd_framebuffer.diminfo[0].shape' may be used uninitialized in this function [-Wmaybe-uninitialized] 7476 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_framebuffer.diminfo[0].shape)) __pyx_t_6 = 0; | ^ x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -fdebug-prefix-map=/build/reproducible-path/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-x86_64-3.9/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-x86_64-3.9/mdtraj/formats/xtc/src/xdrfile_xtc.o build/temp.linux-x86_64-3.9/mdtraj/formats/xtc/xtc.o -o /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/xtc.cpython-39-x86_64-linux-gnu.so building 'mdtraj.formats.trr' extension x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/xtc/src/xdrfile.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_decompress_coord_float': mdtraj/formats/xtc/src/xdrfile.c:788:25: warning: variable 'larger' set but not used [-Wunused-but-set-variable] 788 | int smallnum, smaller, larger, i, is_smaller, run; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c:785:16: warning: variable 'minidx' set but not used [-Wunused-but-set-variable] 785 | int smallidx, minidx, maxidx; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_compress_coord_float': mdtraj/formats/xtc/src/xdrfile.c:1016:6: warning: variable 'errval' set but not used [-Wunused-but-set-variable] 1016 | int errval=1; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_decompress_coord_double': mdtraj/formats/xtc/src/xdrfile.c:1305:25: warning: variable 'larger' set but not used [-Wunused-but-set-variable] 1305 | int smallnum, smaller, larger, i, is_smaller, run; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c:1302:16: warning: variable 'minidx' set but not used [-Wunused-but-set-variable] 1302 | int smallidx, minidx, maxidx; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_compress_coord_double': mdtraj/formats/xtc/src/xdrfile.c:1509:6: warning: variable 'errval' set but not used [-Wunused-but-set-variable] 1509 | int errval=1; | ^~~~~~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/xtc/src/xdrfile_trr.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/xtc/src/xdrfile_trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/xtc/trr.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/xtc/trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1822, 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:4, from mdtraj/formats/xtc/trr.c:639: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ mdtraj/formats/xtc/trr.c: In function '__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_18_write': mdtraj/formats/xtc/trr.c:553:40: warning: '__pyx_v_status' may be used uninitialized in this function [-Wmaybe-uninitialized] 553 | #define PyInt_FromLong PyLong_FromLong | ^~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:10906:7: note: '__pyx_v_status' was declared here 10906 | int __pyx_v_status; | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c: In function '__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_14_read': mdtraj/formats/xtc/trr.c:8259:19: warning: '__pyx_pybuffernd_forces.diminfo[2].shape' may be used uninitialized in this function [-Wmaybe-uninitialized] 8259 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_forces.diminfo[2].shape)) __pyx_t_5 = 2; | ^ mdtraj/formats/xtc/trr.c:8255:19: warning: '__pyx_pybuffernd_forces.diminfo[1].shape' may be used uninitialized in this function [-Wmaybe-uninitialized] 8255 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_forces.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:1775:90: warning: '__pyx_pybuffernd_forces.diminfo[0].strides' may be used uninitialized in this function [-Wmaybe-uninitialized] 1775 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) | ^ mdtraj/formats/xtc/trr.c:6796:21: note: '__pyx_pybuffernd_forces.diminfo[0].strides' was declared here 6796 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8251:19: warning: '__pyx_pybuffernd_forces.diminfo[0].shape' may be used uninitialized in this function [-Wmaybe-uninitialized] 8251 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_forces.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/trr.c:8202:19: warning: '__pyx_pybuffernd_vel.diminfo[2].shape' may be used uninitialized in this function [-Wmaybe-uninitialized] 8202 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_vel.diminfo[2].shape)) __pyx_t_5 = 2; | ^ mdtraj/formats/xtc/trr.c:8198:19: warning: '__pyx_pybuffernd_vel.diminfo[1].shape' may be used uninitialized in this function [-Wmaybe-uninitialized] 8198 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_vel.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:1775:90: warning: '__pyx_pybuffernd_vel.diminfo[0].strides' may be used uninitialized in this function [-Wmaybe-uninitialized] 1775 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) | ^ mdtraj/formats/xtc/trr.c:6812:21: note: '__pyx_pybuffernd_vel.diminfo[0].strides' was declared here 6812 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8194:19: warning: '__pyx_pybuffernd_vel.diminfo[0].shape' may be used uninitialized in this function [-Wmaybe-uninitialized] 8194 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_vel.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/trr.c:8592:17: warning: '__pyx_pybuffernd_xyz_buffer.diminfo[1].shape' may be used uninitialized in this function [-Wmaybe-uninitialized] 8592 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_xyz_buffer.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:8588:17: warning: '__pyx_pybuffernd_xyz_buffer.diminfo[0].shape' may be used uninitialized in this function [-Wmaybe-uninitialized] 8588 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_xyz_buffer.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/trr.c:8433:19: warning: '__pyx_pybuffernd_vel_buffer.diminfo[1].shape' may be used uninitialized in this function [-Wmaybe-uninitialized] 8433 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_vel_buffer.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:8429:19: warning: '__pyx_pybuffernd_vel_buffer.diminfo[0].shape' may be used uninitialized in this function [-Wmaybe-uninitialized] 8429 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_vel_buffer.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/trr.c:8485:19: warning: '__pyx_pybuffernd_forces_buffer.diminfo[1].shape' may be used uninitialized in this function [-Wmaybe-uninitialized] 8485 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_forces_buffer.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:8481:19: warning: '__pyx_pybuffernd_forces_buffer.diminfo[0].shape' may be used uninitialized in this function [-Wmaybe-uninitialized] 8481 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_forces_buffer.diminfo[0].shape)) __pyx_t_5 = 0; | ^ x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -fdebug-prefix-map=/build/reproducible-path/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-x86_64-3.9/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-x86_64-3.9/mdtraj/formats/xtc/src/xdrfile_trr.o build/temp.linux-x86_64-3.9/mdtraj/formats/xtc/trr.o -o /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/trr.cpython-39-x86_64-linux-gnu.so building 'mdtraj.formats.tng' extension creating build/temp.linux-x86_64-3.9/mdtraj/formats/tng creating build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src creating build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression creating build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/lib x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/bwlzh.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/bwlzh.o x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/bwt.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/bwt.o x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/coder.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/coder.o x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/dict.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/dict.o x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/fixpoint.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/fixpoint.o x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/huffman.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/huffman.o x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/huffmem.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/huffmem.o x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/lz77.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/lz77.o x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/merge_sort.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/merge_sort.o x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/mtf.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/mtf.o mdtraj/formats/tng/src/compression/mtf.c: In function 'Ptngc_comp_conv_to_mtf': mdtraj/formats/tng/src/compression/mtf.c:196:23: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 196 | while (dict[ptr]!=v) | ^~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/rle.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/rle.o mdtraj/formats/tng/src/compression/rle.c: In function 'Ptngc_comp_conv_to_rle': mdtraj/formats/tng/src/compression/rle.c:56:16: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 56 | if (v==vals[i]) | ^~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/tng_compress.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/tng_compress.o x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/vals16.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/vals16.o x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/warnmalloc.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/warnmalloc.o x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/widemuldiv.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/widemuldiv.o x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/xtc2.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/xtc2.o x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/xtc3.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/xtc3.o x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/lib/md5.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/lib/md5.o x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/lib/tng_io.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/lib/tng_io.o mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_block_header_read': mdtraj/formats/tng/src/lib/tng_io.c:1064:57: warning: assignment to 'tng_function_status (*)(struct tng_trajectory * const, int32_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, int *)'} from incompatible pointer type 'tng_function_status (*)(struct tng_trajectory * const, uint32_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, unsigned int *)'} [-Wincompatible-pointer-types] 1064 | tng_data->input_endianness_swap_func_32 = | ^ mdtraj/formats/tng/src/lib/tng_io.c:1073:57: warning: assignment to 'tng_function_status (*)(struct tng_trajectory * const, int64_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, long int *)'} from incompatible pointer type 'tng_function_status (*)(struct tng_trajectory * const, uint64_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, long unsigned int *)'} [-Wincompatible-pointer-types] 1073 | tng_data->input_endianness_swap_func_64 = | ^ mdtraj/formats/tng/src/lib/tng_io.c:1089:57: warning: assignment to 'tng_function_status (*)(struct tng_trajectory * const, int32_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, int *)'} from incompatible pointer type 'tng_function_status (*)(struct tng_trajectory * const, uint32_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, unsigned int *)'} [-Wincompatible-pointer-types] 1089 | tng_data->input_endianness_swap_func_32 = | ^ mdtraj/formats/tng/src/lib/tng_io.c:1098:57: warning: assignment to 'tng_function_status (*)(struct tng_trajectory * const, int64_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, long int *)'} from incompatible pointer type 'tng_function_status (*)(struct tng_trajectory * const, uint64_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, long unsigned int *)'} [-Wincompatible-pointer-types] 1098 | tng_data->input_endianness_swap_func_64 = | ^ mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_output_file_endianness_get': mdtraj/formats/tng/src/lib/tng_io.c:9565:53: warning: comparison of distinct pointer types lacks a cast 9565 | if(tng_data->output_endianness_swap_func_32 == | ^~ mdtraj/formats/tng/src/lib/tng_io.c:9570:58: warning: comparison of distinct pointer types lacks a cast 9570 | else if(tng_data->output_endianness_swap_func_32 == | ^~ mdtraj/formats/tng/src/lib/tng_io.c:9588:53: warning: comparison of distinct pointer types lacks a cast 9588 | if(tng_data->output_endianness_swap_func_64 == | ^~ mdtraj/formats/tng/src/lib/tng_io.c:9593:58: warning: comparison of distinct pointer types lacks a cast 9593 | else if(tng_data->output_endianness_swap_func_64 == | ^~ mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_output_file_endianness_set': mdtraj/formats/tng/src/lib/tng_io.c:9651:54: warning: assignment to 'tng_function_status (*)(struct tng_trajectory * const, int32_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, int *)'} from incompatible pointer type 'tng_function_status (*)(struct tng_trajectory * const, uint32_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, unsigned int *)'} [-Wincompatible-pointer-types] 9651 | tng_data->output_endianness_swap_func_32 = | ^ mdtraj/formats/tng/src/lib/tng_io.c:9660:54: warning: assignment to 'tng_function_status (*)(struct tng_trajectory * const, int64_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, long int *)'} from incompatible pointer type 'tng_function_status (*)(struct tng_trajectory * const, uint64_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, long unsigned int *)'} [-Wincompatible-pointer-types] 9660 | tng_data->output_endianness_swap_func_64 = | ^ mdtraj/formats/tng/src/lib/tng_io.c:9673:54: warning: assignment to 'tng_function_status (*)(struct tng_trajectory * const, int32_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, int *)'} from incompatible pointer type 'tng_function_status (*)(struct tng_trajectory * const, uint32_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, unsigned int *)'} [-Wincompatible-pointer-types] 9673 | tng_data->output_endianness_swap_func_32 = | ^ mdtraj/formats/tng/src/lib/tng_io.c:9682:54: warning: assignment to 'tng_function_status (*)(struct tng_trajectory * const, int64_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, long int *)'} from incompatible pointer type 'tng_function_status (*)(struct tng_trajectory * const, uint64_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, long unsigned int *)'} [-Wincompatible-pointer-types] 9682 | tng_data->output_endianness_swap_func_64 = | ^ In file included from /usr/include/string.h:495, from mdtraj/formats/tng/include/tng/tng_io.h:302, from mdtraj/formats/tng/src/lib/tng_io.c:20: In function 'strncpy', inlined from 'tng_gen_data_block_add' at mdtraj/formats/tng/src/lib/tng_io.c:12613:9: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_gen_data_block_add': mdtraj/formats/tng/src/lib/tng_io.c:12613:47: note: length computed here 12613 | strncpy(data->block_name, block_name, strlen(block_name) + 1); | ^~~~~~~~~~~~~~~~~~ mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_data_block_write.isra': mdtraj/formats/tng/src/lib/tng_io.c:5986:72: warning: 'num_first_particle' may be used uninitialized in this function [-Wmaybe-uninitialized] 5986 | for(j = num_first_particle; j < num_first_particle + n_particles; | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ mdtraj/formats/tng/src/lib/tng_io.c:4308:24: warning: 'n_particles' may be used uninitialized in this function [-Wmaybe-uninitialized] 4308 | dest = tng_compress_pos_float((float *)*data, (int)n_particles, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 4309 | (int)n_frames, | ~~~~~~~~~~~~~~ 4310 | f_precision, | ~~~~~~~~~~~~ 4311 | 0, alt_algo, | ~~~~~~~~~~~~ 4312 | &compressed_len); | ~~~~~~~~~~~~~~~~ mdtraj/formats/tng/src/lib/tng_io.c:5684:13: note: 'n_particles' was declared here 5684 | int64_t n_particles, num_first_particle, n_frames, stride_length; | ^~~~~~~~~~~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/tng.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/tng.o In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1822, 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:4, from mdtraj/formats/tng/tng.c:665: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ mdtraj/formats/tng/tng.c: In function '__pyx_pf_6mdtraj_7formats_3tng_17TNGTrajectoryFile___cinit__': mdtraj/formats/tng/tng.c:3541:104: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3541 | __pyx_t_1 = ((tng_util_trajectory_open(__pyx_v_filename, __pyx_v_self->mode, (&__pyx_v_self->_traj)) == __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:3596:88: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3596 | __pyx_t_1 = ((tng_num_particles_get(__pyx_v_self->_traj, (&__pyx_v_self->n_atoms)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:3628:90: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3628 | __pyx_t_1 = ((tng_num_frames_get(__pyx_v_self->_traj, (&__pyx_v_self->tot_n_frames)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:3660:95: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3660 | __pyx_t_1 = ((tng_distance_unit_exponential_get(__pyx_v_self->_traj, (&__pyx_v_exponent)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:3730:113: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3730 | __pyx_t_1 = ((tng_num_frames_per_frame_set_get(__pyx_v_self->_traj, (&__pyx_v_self->_frames_per_frame_set)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:3774:77: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3774 | __pyx_t_1 = ((tng_last_program_name_set(__pyx_v_self->_traj, __pyx_t_8) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c: In function '__pyx_pf_6mdtraj_7formats_3tng_17TNGTrajectoryFile_8_read_topology': mdtraj/formats/tng/tng.c:4568:106: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 4568 | __pyx_t_7 = ((tng_chain_name_of_particle_nr_get(__pyx_v_self->_traj, __pyx_v_i, __pyx_v_text, 0x400) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:4613:108: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 4613 | __pyx_t_7 = ((tng_residue_name_of_particle_nr_get(__pyx_v_self->_traj, __pyx_v_i, __pyx_v_text, 0x400) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:4720:115: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 4720 | __pyx_t_8 = ((tng_global_residue_id_of_particle_nr_get(__pyx_v_self->_traj, __pyx_v_i, (&__pyx_v_residue_id)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:4750:105: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 4750 | __pyx_t_8 = ((tng_atom_name_of_particle_nr_get(__pyx_v_self->_traj, __pyx_v_i, __pyx_v_text, 0x400) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:4878:105: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 4878 | __pyx_t_8 = ((tng_atom_type_of_particle_nr_get(__pyx_v_self->_traj, __pyx_v_i, __pyx_v_text, 0x400) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:5479:126: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 5479 | __pyx_t_7 = ((tng_molsystem_bonds_get(__pyx_v_self->_traj, (&__pyx_v_n_bonds), (&__pyx_v_from_atoms), (&__pyx_v_to_atoms)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c: In function '__pyx_pf_6mdtraj_7formats_3tng_17TNGTrajectoryFile_10_read_frame': mdtraj/formats/tng/tng.c:5887:152: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 5887 | __pyx_t_1 = ((tng_util_pos_read_range(__pyx_v_self->_traj, __pyx_v_self->_pos, __pyx_v_self->_pos, (&__pyx_v_positions), (&__pyx_v_stride_length)) == __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:6155:108: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 6155 | __pyx_t_1 = ((tng_util_time_of_frame_get(__pyx_v_self->_traj, __pyx_v_self->_pos, (&__pyx_v_frame_time)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:6257:304: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 6257 | __pyx_t_1 = ((tng_data_vector_interval_get(__pyx_v_self->_traj, __pyx_v_6mdtraj_7formats_3tng_TNG_TRAJ_BOX_SHAPE, __pyx_v_self->_pos, __pyx_v_self->_pos, __pyx_e_6mdtraj_7formats_3tng_TNG_USE_HASH, (&__pyx_v_box_shape), (&__pyx_v_stride_length), (&__pyx_v_n_values_per_frame), (&__pyx_v_data_type)) == __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c: In function '__pyx_pf_6mdtraj_7formats_3tng_17TNGTrajectoryFile_16write': mdtraj/formats/tng/tng.c:8747:94: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 8747 | __pyx_t_1 = ((tng_implicit_num_particles_set(__pyx_v_self->_traj, __pyx_v_self->n_atoms) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:8779:75: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 8779 | __pyx_t_1 = ((tng_util_pos_write_interval_set(__pyx_v_self->_traj, 1) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:8811:81: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 8811 | __pyx_t_1 = ((tng_util_box_shape_write_interval_set(__pyx_v_self->_traj, 1) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:9134:77: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 9134 | __pyx_t_9 = ((tng_time_per_frame_set(__pyx_v_self->_traj, __pyx_t_15) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:9325:372: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 9325 | __pyx_t_1 = ((tng_util_pos_write(__pyx_v_self->_traj, __pyx_v_self->tot_n_frames, (&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_xyz_array.rcbuffer->pybuffer.buf, __pyx_t_18, __pyx_pybuffernd_xyz_array.diminfo[0].strides, __pyx_t_19, __pyx_pybuffernd_xyz_array.diminfo[1].strides, __pyx_t_20, __pyx_pybuffernd_xyz_array.diminfo[2].strides)))) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:9377:378: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 9377 | __pyx_t_1 = ((tng_util_box_shape_write(__pyx_v_self->_traj, __pyx_v_self->tot_n_frames, (&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_box_array.rcbuffer->pybuffer.buf, __pyx_t_20, __pyx_pybuffernd_box_array.diminfo[0].strides, __pyx_t_19, __pyx_pybuffernd_box_array.diminfo[1].strides, __pyx_t_18, __pyx_pybuffernd_box_array.diminfo[2].strides)))) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:9439:89: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 9439 | __pyx_t_1 = ((tng_frame_set_first_frame_time_set(__pyx_v_self->_traj, __pyx_t_15) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -fdebug-prefix-map=/build/reproducible-path/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/bwlzh.o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/bwt.o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/coder.o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/dict.o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/fixpoint.o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/huffman.o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/huffmem.o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/lz77.o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/merge_sort.o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/mtf.o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/rle.o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/tng_compress.o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/vals16.o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/warnmalloc.o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/widemuldiv.o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/xtc2.o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/xtc3.o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/lib/md5.o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/lib/tng_io.o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/tng.o -lz -o /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/tng.cpython-39-x86_64-linux-gnu.so building 'mdtraj.formats.dcd' extension creating build/temp.linux-x86_64-3.9/mdtraj/formats/dcd creating build/temp.linux-x86_64-3.9/mdtraj/formats/dcd/src x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/dcd/include/ -Imdtraj/formats/dcd/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/dcd/dcd.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/dcd/dcd.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1822, 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:4, from mdtraj/formats/dcd/dcd.c:637: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ mdtraj/formats/dcd/dcd.c: In function '__pyx_pf_6mdtraj_7formats_3dcd_17DCDTrajectoryFile_20read': mdtraj/formats/dcd/dcd.c:551:40: warning: '__pyx_v_i' may be used uninitialized in this function [-Wmaybe-uninitialized] 551 | #define PyInt_FromLong PyLong_FromLong | ^~~~~~~~~~~~~~~ mdtraj/formats/dcd/dcd.c:5280:7: note: '__pyx_v_i' was declared here 5280 | int __pyx_v_i; | ^~~~~~~~~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/dcd/include/ -Imdtraj/formats/dcd/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/dcd/src/dcdplugin.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/dcd/src/dcdplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -fdebug-prefix-map=/build/reproducible-path/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/mdtraj/formats/dcd/dcd.o build/temp.linux-x86_64-3.9/mdtraj/formats/dcd/src/dcdplugin.o -o /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/dcd.cpython-39-x86_64-linux-gnu.so building 'mdtraj.formats.binpos' extension creating build/temp.linux-x86_64-3.9/mdtraj/formats/binpos creating build/temp.linux-x86_64-3.9/mdtraj/formats/binpos/src x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/binpos/include/ -Imdtraj/formats/binpos/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/binpos/binpos.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/binpos/binpos.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1822, 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:4, from mdtraj/formats/binpos/binpos.c:637: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ mdtraj/formats/binpos/binpos.c: In function '__pyx_pw_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_9_read': mdtraj/formats/binpos/binpos.c:5355:6: warning: '__pyx_v_status' may be used uninitialized in this function [-Wmaybe-uninitialized] 5355 | if (__pyx_t_2) { | ^ mdtraj/formats/binpos/binpos.c:4835:7: note: '__pyx_v_status' was declared here 4835 | int __pyx_v_status; | ^~~~~~~~~~~~~~ mdtraj/formats/binpos/binpos.c:551:40: warning: '__pyx_v_i' may be used uninitialized in this function [-Wmaybe-uninitialized] 551 | #define PyInt_FromLong PyLong_FromLong | ^~~~~~~~~~~~~~~ mdtraj/formats/binpos/binpos.c:4832:7: note: '__pyx_v_i' was declared here 4832 | int __pyx_v_i; | ^~~~~~~~~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/binpos/include/ -Imdtraj/formats/binpos/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/binpos/src/binposplugin.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/binpos/src/binposplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -fdebug-prefix-map=/build/reproducible-path/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/mdtraj/formats/binpos/binpos.o build/temp.linux-x86_64-3.9/mdtraj/formats/binpos/src/binposplugin.o -o /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/binpos.cpython-39-x86_64-linux-gnu.so building 'mdtraj.formats.dtr' extension creating build/temp.linux-x86_64-3.9/mdtraj/formats/dtr creating build/temp.linux-x86_64-3.9/mdtraj/formats/dtr/src x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/dtr/dtr.cpp -o build/temp.linux-x86_64-3.9/mdtraj/formats/dtr/dtr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1822, 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:4, from mdtraj/formats/dtr/dtr.cpp:658: /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 " \ | ^~~~~~~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/dtr/src/dtrplugin.cxx -o build/temp.linux-x86_64-3.9/mdtraj/formats/dtr/src/dtrplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/formats/dtr/src/dtrplugin.cxx: In member function 'bool desres::molfile::Timekeys::init(const string&)': mdtraj/formats/dtr/src/dtrplugin.cxx:487:27: warning: format '%d' expects argument of type 'int', but argument 2 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] 487 | printf("size %d framesize %d\n\n", | ~^ | | | int | %ld 488 | keys[i].size(), m_framesize); | ~~~~~~~~~~~~~~ | | | uint64_t {aka long unsigned int} mdtraj/formats/dtr/src/dtrplugin.cxx:487:40: warning: format '%d' expects argument of type 'int', but argument 3 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] 487 | printf("size %d framesize %d\n\n", | ~^ | | | int | %ld 488 | keys[i].size(), m_framesize); | ~~~~~~~~~~~ | | | uint64_t {aka long unsigned int} mdtraj/formats/dtr/src/dtrplugin.cxx: In constructor '{anonymous}::DDException::DDException(const string&, int)': mdtraj/formats/dtr/src/dtrplugin.cxx:680:43: warning: '*.{anonymous}::DDException::eno' is used uninitialized in this function [-Wuninitialized] 680 | : std::runtime_error(text + strerror(eno)), eno(_eno){} | ~~~~~~~~^~~~~ mdtraj/formats/dtr/src/dtrplugin.cxx: In function 'void DDmkdir(const string&, mode_t, int, int)': mdtraj/formats/dtr/src/dtrplugin.cxx:706:16: warning: '%03x' directive writing between 3 and 8 bytes into a region of size 6 [-Wformat-overflow=] 706 | sprintf(sub, "%03x/", i); | ^~~~ mdtraj/formats/dtr/src/dtrplugin.cxx:706:15: note: directive argument in the range [0, 2147483646] 706 | sprintf(sub, "%03x/", i); | ^~~~~~~ In file included from /usr/include/stdio.h:867, from mdtraj/formats/dtr/include/molfile_plugin.h:35, from mdtraj/formats/dtr/include/dtrplugin.hxx:46, from mdtraj/formats/dtr/src/dtrplugin.cxx:42: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 5 and 10 bytes into a destination of size 6 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/dtr/src/dtrplugin.cxx:714:23: warning: '%03x' directive writing between 3 and 8 bytes into a region of size 6 [-Wformat-overflow=] 714 | sprintf(subsub, "%03x", j); | ^~~~ mdtraj/formats/dtr/src/dtrplugin.cxx:714:22: note: directive argument in the range [0, 2147483646] 714 | sprintf(subsub, "%03x", j); | ^~~~~~ In file included from /usr/include/stdio.h:867, from mdtraj/formats/dtr/include/molfile_plugin.h:35, from mdtraj/formats/dtr/include/dtrplugin.hxx:46, from mdtraj/formats/dtr/src/dtrplugin.cxx:42: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 4 and 9 bytes into a destination of size 6 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/dtr/src/dtrplugin.cxx: In function 'std::string framefile(const string&, size_t, size_t, int, int)': mdtraj/formats/dtr/src/dtrplugin.cxx:667:28: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=] 667 | sprintf(answer, "%03x/", d1); | ^ In file included from /usr/include/stdio.h:867, from mdtraj/formats/dtr/include/molfile_plugin.h:35, from mdtraj/formats/dtr/include/dtrplugin.hxx:46, from mdtraj/formats/dtr/src/dtrplugin.cxx:42: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 5 and 10 bytes into a destination of size 9 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/dtr/src/dtrplugin.cxx:665:28: warning: '%03x' directive writing between 3 and 8 bytes into a region of size between 0 and 5 [-Wformat-overflow=] 665 | sprintf(answer, "%03x/%03x/", d1, d2); | ^~~~ mdtraj/formats/dtr/src/dtrplugin.cxx:665:22: note: directive argument in the range [0, 2147483646] 665 | sprintf(answer, "%03x/%03x/", d1, d2); | ^~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from mdtraj/formats/dtr/include/molfile_plugin.h:35, from mdtraj/formats/dtr/include/dtrplugin.hxx:46, from mdtraj/formats/dtr/src/dtrplugin.cxx:42: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 9 and 19 bytes into a destination of size 9 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -fdebug-prefix-map=/build/reproducible-path/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/mdtraj/formats/dtr/dtr.o build/temp.linux-x86_64-3.9/mdtraj/formats/dtr/src/dtrplugin.o -o /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/dtr.cpython-39-x86_64-linux-gnu.so building 'mdtraj._rmsd' extension creating build/temp.linux-x86_64-3.9/mdtraj/rmsd creating build/temp.linux-x86_64-3.9/mdtraj/rmsd/src x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/_rmsd.cpp -o build/temp.linux-x86_64-3.9/mdtraj/rmsd/_rmsd.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/rmsd/_rmsd.cpp: In function 'int __Pyx_InitGlobals()': mdtraj/rmsd/_rmsd.cpp:24626:20: warning: 'void PyEval_InitThreads()' is deprecated [-Wdeprecated-declarations] 24626 | PyEval_InitThreads(); | ^ In file included from /usr/include/python3.9/Python.h:145, from mdtraj/rmsd/_rmsd.cpp:40: /usr/include/python3.9/ceval.h:130:37: note: declared here 130 | Py_DEPRECATED(3.9) PyAPI_FUNC(void) PyEval_InitThreads(void); | ^~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-x86_64-3.9/mdtraj/rmsd/src/center.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/src/rotation.cpp -o build/temp.linux-x86_64-3.9/mdtraj/rmsd/src/rotation.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-x86_64-3.9/mdtraj/rmsd/src/theobald_rmsd.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -fdebug-prefix-map=/build/reproducible-path/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/mdtraj/rmsd/_rmsd.o build/temp.linux-x86_64-3.9/mdtraj/rmsd/src/center.o build/temp.linux-x86_64-3.9/mdtraj/rmsd/src/rotation.o build/temp.linux-x86_64-3.9/mdtraj/rmsd/src/theobald_rmsd.o -lgomp -o /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/_rmsd.cpython-39-x86_64-linux-gnu.so building 'mdtraj._lprmsd' extension x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/_lprmsd.cpp -o build/temp.linux-x86_64-3.9/mdtraj/rmsd/_lprmsd.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1822, 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:4, from mdtraj/rmsd/_lprmsd.cpp:668: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ mdtraj/rmsd/_lprmsd.cpp: In function 'int __Pyx_InitGlobals()': mdtraj/rmsd/_lprmsd.cpp:9166:20: warning: 'void PyEval_InitThreads()' is deprecated [-Wdeprecated-declarations] 9166 | PyEval_InitThreads(); | ^ In file included from /usr/include/python3.9/Python.h:145, from mdtraj/rmsd/_lprmsd.cpp:48: /usr/include/python3.9/ceval.h:130:37: note: declared here 130 | Py_DEPRECATED(3.9) PyAPI_FUNC(void) PyEval_InitThreads(void); | ^~~~~~~~~~~~~~~~~~ mdtraj/rmsd/_lprmsd.cpp: In function 'PyObject* __pyx_pf_6mdtraj_7_lprmsd_lprmsd(PyObject*, PyObject*, PyObject*, int, PyObject*, PyObject*, PyLongObject*, PyLongObject*)': mdtraj/rmsd/_lprmsd.cpp:3964:14: warning: '__pyx_pybuffernd_ref_xyz_frame_dis.__Pyx_LocalBuf_ND::diminfo[0].__Pyx_Buf_DimInfo::shape' may be used uninitialized in this function [-Wmaybe-uninitialized] 3964 | } else if (unlikely(__pyx_t_34 >= __pyx_pybuffernd_ref_xyz_frame_dis.diminfo[0].shape)) __pyx_t_33 = 0; | ^~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/src/Munkres.cpp -o build/temp.linux-x86_64-3.9/mdtraj/rmsd/src/Munkres.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-x86_64-3.9/mdtraj/rmsd/src/center.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/src/euclidean_permutation.cpp -o build/temp.linux-x86_64-3.9/mdtraj/rmsd/src/euclidean_permutation.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/src/fancy_index.cpp -o build/temp.linux-x86_64-3.9/mdtraj/rmsd/src/fancy_index.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/src/rotation.cpp -o build/temp.linux-x86_64-3.9/mdtraj/rmsd/src/rotation.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-x86_64-3.9/mdtraj/rmsd/src/theobald_rmsd.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -fdebug-prefix-map=/build/reproducible-path/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/mdtraj/rmsd/_lprmsd.o build/temp.linux-x86_64-3.9/mdtraj/rmsd/src/Munkres.o build/temp.linux-x86_64-3.9/mdtraj/rmsd/src/center.o build/temp.linux-x86_64-3.9/mdtraj/rmsd/src/euclidean_permutation.o build/temp.linux-x86_64-3.9/mdtraj/rmsd/src/fancy_index.o build/temp.linux-x86_64-3.9/mdtraj/rmsd/src/rotation.o build/temp.linux-x86_64-3.9/mdtraj/rmsd/src/theobald_rmsd.o -lgomp -o /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/_lprmsd.cpython-39-x86_64-linux-gnu.so building 'mdtraj.core.lib.libtheobald' extension x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-x86_64-3.9/mdtraj/rmsd/src/theobald_rmsd.o -msse2 -mssse3 -O3 -funroll-loops x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-x86_64-3.9/mdtraj/rmsd/src/center.o -msse2 -mssse3 -O3 -funroll-loops x86_64-linux-gnu-gcc-ar rcs /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/core/lib/libtheobald.a build/temp.linux-x86_64-3.9/mdtraj/rmsd/src/theobald_rmsd.o build/temp.linux-x86_64-3.9/mdtraj/rmsd/src/center.o building 'mdtraj.geometry._geometry' extension creating build/temp.linux-x86_64-3.9/mdtraj/geometry creating build/temp.linux-x86_64-3.9/mdtraj/geometry/src x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/geometry/src/_geometry.cpp -o build/temp.linux-x86_64-3.9/mdtraj/geometry/src/_geometry.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1822, 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:4, from mdtraj/geometry/src/_geometry.cpp:670: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ mdtraj/geometry/src/_geometry.cpp: In function 'void __pyx_f_6mdtraj_8geometry_9_geometry_make_whole(__Pyx_memviewslice, __Pyx_memviewslice, __Pyx_memviewslice)': mdtraj/geometry/src/_geometry.cpp:5506:224: warning: '__pyx_v_delta[2]' may be used uninitialized in this function [-Wmaybe-uninitialized] 5506 | (__pyx_v_offset[__pyx_v_k]) = ((*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_frame_unitcell_vectors.data + __pyx_t_8 * __pyx_v_frame_unitcell_vectors.strides[0]) )) + __pyx_t_7)) ))) * roundf(((__pyx_v_delta[2]) / (*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_frame_unitcell_vectors.data + __pyx_t_5 * __pyx_v_frame_unitcell_vectors.strides[0]) )) + __pyx_t_4)) )))))); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/geometry/src/_geometry.cpp:5520:277: warning: '__pyx_v_delta[1]' may be used uninitialized in this function [-Wmaybe-uninitialized] 5520 | (__pyx_v_offset[__pyx_t_9]) = ((__pyx_v_offset[__pyx_t_9]) + ((*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_frame_unitcell_vectors.data + __pyx_t_4 * __pyx_v_frame_unitcell_vectors.strides[0]) )) + __pyx_t_5)) ))) * roundf((((__pyx_v_delta[1]) - (__pyx_v_offset[1])) / (*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_frame_unitcell_vectors.data + __pyx_t_7 * __pyx_v_frame_unitcell_vectors.strides[0]) )) + __pyx_t_8)) ))))))); | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ mdtraj/geometry/src/_geometry.cpp:5520:277: warning: '__pyx_v_offset[1]' may be used uninitialized in this function [-Wmaybe-uninitialized] x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/geometry/src/dssp.cpp -o build/temp.linux-x86_64-3.9/mdtraj/geometry/src/dssp.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/geometry/src/geometry.cpp -o build/temp.linux-x86_64-3.9/mdtraj/geometry/src/geometry.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/geometry/src/sasa.cpp -o build/temp.linux-x86_64-3.9/mdtraj/geometry/src/sasa.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -fdebug-prefix-map=/build/reproducible-path/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/mdtraj/geometry/src/_geometry.o build/temp.linux-x86_64-3.9/mdtraj/geometry/src/dssp.o build/temp.linux-x86_64-3.9/mdtraj/geometry/src/geometry.o build/temp.linux-x86_64-3.9/mdtraj/geometry/src/sasa.o -lgomp -o /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/_geometry.cpython-39-x86_64-linux-gnu.so building 'mdtraj.geometry.drid' extension x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/geometry/drid.cpp -o build/temp.linux-x86_64-3.9/mdtraj/geometry/drid.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/geometry/drid.cpp: In function 'int __Pyx_InitGlobals()': mdtraj/geometry/drid.cpp:18465:20: warning: 'void PyEval_InitThreads()' is deprecated [-Wdeprecated-declarations] 18465 | PyEval_InitThreads(); | ^ In file included from /usr/include/python3.9/Python.h:145, from mdtraj/geometry/drid.cpp:39: /usr/include/python3.9/ceval.h:130:37: note: declared here 130 | Py_DEPRECATED(3.9) PyAPI_FUNC(void) PyEval_InitThreads(void); | ^~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/geometry/src/dridkernels.cpp -o build/temp.linux-x86_64-3.9/mdtraj/geometry/src/dridkernels.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/geometry/src/moments.cpp -o build/temp.linux-x86_64-3.9/mdtraj/geometry/src/moments.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -fdebug-prefix-map=/build/reproducible-path/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/mdtraj/geometry/drid.o build/temp.linux-x86_64-3.9/mdtraj/geometry/src/dridkernels.o build/temp.linux-x86_64-3.9/mdtraj/geometry/src/moments.o -lgomp -o /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/drid.cpython-39-x86_64-linux-gnu.so building 'mdtraj.geometry.neighbors' extension x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/geometry/neighbors.cpp -o build/temp.linux-x86_64-3.9/mdtraj/geometry/neighbors.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/geometry/src/neighbors.cpp -o build/temp.linux-x86_64-3.9/mdtraj/geometry/src/neighbors.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -fdebug-prefix-map=/build/reproducible-path/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/mdtraj/geometry/neighbors.o build/temp.linux-x86_64-3.9/mdtraj/geometry/src/neighbors.o -lgomp -o /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/neighbors.cpython-39-x86_64-linux-gnu.so building 'mdtraj.geometry.neighborlist' extension x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/geometry/neighborlist.cpp -o build/temp.linux-x86_64-3.9/mdtraj/geometry/neighborlist.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/geometry/src/neighborlist.cpp -o build/temp.linux-x86_64-3.9/mdtraj/geometry/src/neighborlist.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/geometry/src/neighborlist.cpp: In function 'std::vector > _compute_neighborlist(const float*, int, float, const float*)': mdtraj/geometry/src/neighborlist.cpp:50:53: warning: 'periodicBoxVectors[0][0]' may be used uninitialized in this function [-Wmaybe-uninitialized] 50 | periodicBoxSize[0] = periodicBoxVectors[0][0]; | ~~~~~~~~~~~~~~~~~~~~~~~^ mdtraj/geometry/src/neighborlist.cpp:51:53: warning: 'periodicBoxVectors[1][1]' may be used uninitialized in this function [-Wmaybe-uninitialized] 51 | periodicBoxSize[1] = periodicBoxVectors[1][1]; | ~~~~~~~~~~~~~~~~~~~~~~~^ mdtraj/geometry/src/neighborlist.cpp:52:53: warning: 'periodicBoxVectors[2][2]' may be used uninitialized in this function [-Wmaybe-uninitialized] 52 | periodicBoxSize[2] = periodicBoxVectors[2][2]; | ~~~~~~~~~~~~~~~~~~~~~~~^ mdtraj/geometry/src/neighborlist.cpp:56:45: warning: 'periodicBoxVectors[0][1]' may be used uninitialized in this function [-Wmaybe-uninitialized] 56 | triclinic = (periodicBoxVectors[0][1] != 0.0 || periodicBoxVectors[0][2] != 0.0 || | ~~~~~~~~~~~~~~~~~~~~~~~^ x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -fdebug-prefix-map=/build/reproducible-path/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/mdtraj/geometry/neighborlist.o build/temp.linux-x86_64-3.9/mdtraj/geometry/src/neighborlist.o -lgomp -o /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/neighborlist.cpython-39-x86_64-linux-gnu.so cp -a /build/reproducible-path/mdtraj-1.9.5/examples /build/reproducible-path/mdtraj-1.9.5/examples.orig mkdir -p /build/reproducible-path/mdtraj-1.9.5/build/html/examples/iterload ln -s /build/reproducible-path/mdtraj-1.9.5/examples/data /build/reproducible-path/mdtraj-1.9.5/build/html/examples/iterload/data sed "s|http://www.rcsb.org/pdb/files|/build/reproducible-path/mdtraj-1.9.5/debian/external|g" -i /build/reproducible-path/mdtraj-1.9.5/examples/*.ipynb PYTHONPATH=/build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build \ MPLCONFIGDIR=/build/reproducible-path/mdtraj-1.9.5/build/matplotlib \ make -C docs BUILDDIR=/build/reproducible-path/mdtraj-1.9.5/build html make[2]: Entering directory '/build/reproducible-path/mdtraj-1.9.5/docs' sphinx-build -b html -d /build/reproducible-path/mdtraj-1.9.5/build/doctrees . /build/reproducible-path/mdtraj-1.9.5/build/html Running Sphinx v3.4.3 [autosummary] generating autosummary for: analysis.rst, api/reporters.rst, api/trajectory_files.rst, api/utils.rst, atom_selection.rst, building_docs.rst, examples/atom-selection.rst, examples/centroids.rst, examples/clustering.rst, examples/hbonds.rst, ..., examples/solvent-accessible-surface-area.rst, examples/two-pass-clustering.rst, faq.rst, hdf5_format.rst, index.rst, installation.rst, load_functions.rst, mdconvert.rst, new_to_python.rst, whatsnew.rst [autosummary] generating autosummary for: /build/reproducible-path/mdtraj-1.9.5/docs/api/generated/mdtraj.Topology.rst, /build/reproducible-path/mdtraj-1.9.5/docs/api/generated/mdtraj.Trajectory.rst, /build/reproducible-path/mdtraj-1.9.5/docs/api/generated/mdtraj.Trajectory.superpose.rst, /build/reproducible-path/mdtraj-1.9.5/docs/api/generated/mdtraj.acylindricity.rst, /build/reproducible-path/mdtraj-1.9.5/docs/api/generated/mdtraj.asphericity.rst, /build/reproducible-path/mdtraj-1.9.5/docs/api/generated/mdtraj.baker_hubbard.rst, /build/reproducible-path/mdtraj-1.9.5/docs/api/generated/mdtraj.chemical_shifts_ppm.rst, /build/reproducible-path/mdtraj-1.9.5/docs/api/generated/mdtraj.chemical_shifts_shiftx2.rst, /build/reproducible-path/mdtraj-1.9.5/docs/api/generated/mdtraj.chemical_shifts_spartaplus.rst, /build/reproducible-path/mdtraj-1.9.5/docs/api/generated/mdtraj.compute_J3_HN_C.rst, ..., /build/reproducible-path/mdtraj-1.9.5/docs/api/generated/mdtraj.utils.check_random_state.rst, /build/reproducible-path/mdtraj-1.9.5/docs/api/generated/mdtraj.utils.ensure_type.rst, /build/reproducible-path/mdtraj-1.9.5/docs/api/generated/mdtraj.utils.ilen.rst, /build/reproducible-path/mdtraj-1.9.5/docs/api/generated/mdtraj.utils.import_.rst, /build/reproducible-path/mdtraj-1.9.5/docs/api/generated/mdtraj.utils.in_units_of.rst, /build/reproducible-path/mdtraj-1.9.5/docs/api/generated/mdtraj.utils.lengths_and_angles_to_box_vectors.rst, /build/reproducible-path/mdtraj-1.9.5/docs/api/generated/mdtraj.utils.rotation_matrix_from_quaternion.rst, /build/reproducible-path/mdtraj-1.9.5/docs/api/generated/mdtraj.utils.timing.rst, /build/reproducible-path/mdtraj-1.9.5/docs/api/generated/mdtraj.utils.uniform_quaternion.rst, /build/reproducible-path/mdtraj-1.9.5/docs/api/generated/mdtraj.wernet_nilsson.rst building [mo]: targets for 0 po files that are out of date building [html]: targets for 29 source files that are out of date updating environment: [new config] 127 added, 0 changed, 0 removed reading sources... [ 0%] analysis reading sources... [ 1%] api/generated/mdtraj.Topology reading sources... [ 2%] api/generated/mdtraj.Trajectory reading sources... [ 3%] api/generated/mdtraj.Trajectory.superpose reading sources... [ 3%] api/generated/mdtraj.acylindricity reading sources... [ 4%] api/generated/mdtraj.asphericity reading sources... [ 5%] api/generated/mdtraj.baker_hubbard reading sources... [ 6%] api/generated/mdtraj.chemical_shifts_ppm reading sources... [ 7%] api/generated/mdtraj.chemical_shifts_shiftx2 reading sources... [ 7%] api/generated/mdtraj.chemical_shifts_spartaplus reading sources... [ 8%] api/generated/mdtraj.compute_J3_HN_C reading sources... [ 9%] api/generated/mdtraj.compute_J3_HN_CB reading sources... [ 10%] api/generated/mdtraj.compute_J3_HN_HA reading sources... [ 11%] api/generated/mdtraj.compute_angles reading sources... [ 11%] api/generated/mdtraj.compute_center_of_mass reading sources... [ 12%] api/generated/mdtraj.compute_chi1 reading sources... [ 13%] api/generated/mdtraj.compute_chi2 reading sources... [ 14%] api/generated/mdtraj.compute_chi3 reading sources... [ 14%] api/generated/mdtraj.compute_chi4 reading sources... [ 15%] api/generated/mdtraj.compute_contacts reading sources... [ 16%] api/generated/mdtraj.compute_dihedrals reading sources... [ 17%] api/generated/mdtraj.compute_directors reading sources... [ 18%] api/generated/mdtraj.compute_displacements reading sources... [ 18%] api/generated/mdtraj.compute_distances reading sources... [ 19%] api/generated/mdtraj.compute_drid reading sources... [ 20%] api/generated/mdtraj.compute_dssp reading sources... [ 21%] api/generated/mdtraj.compute_gyration_tensor reading sources... [ 22%] api/generated/mdtraj.compute_inertia_tensor reading sources... [ 22%] api/generated/mdtraj.compute_neighbors reading sources... [ 23%] api/generated/mdtraj.compute_nematic_order reading sources... [ 24%] api/generated/mdtraj.compute_omega reading sources... [ 25%] api/generated/mdtraj.compute_phi reading sources... [ 25%] api/generated/mdtraj.compute_psi reading sources... [ 26%] api/generated/mdtraj.compute_rdf reading sources... [ 27%] api/generated/mdtraj.compute_rg reading sources... [ 28%] api/generated/mdtraj.density reading sources... [ 29%] api/generated/mdtraj.dipole_moments reading sources... [ 29%] api/generated/mdtraj.formats.AmberNetCDFRestartFile reading sources... [ 30%] api/generated/mdtraj.formats.AmberRestartFile reading sources... [ 31%] api/generated/mdtraj.formats.ArcTrajectoryFile reading sources... [ 32%] api/generated/mdtraj.formats.BINPOSTrajectoryFile reading sources... [ 33%] api/generated/mdtraj.formats.DCDTrajectoryFile reading sources... [ 33%] api/generated/mdtraj.formats.DTRTrajectoryFile reading sources... [ 34%] api/generated/mdtraj.formats.GroTrajectoryFile reading sources... [ 35%] api/generated/mdtraj.formats.HDF5TrajectoryFile reading sources... 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[ 60%] api/generated/mdtraj.open reading sources... [ 61%] api/generated/mdtraj.principal_moments reading sources... [ 62%] api/generated/mdtraj.reindex_dataframe_by_atoms reading sources... [ 62%] api/generated/mdtraj.relative_shape_antisotropy reading sources... [ 63%] api/generated/mdtraj.reporters.DCDReporter reading sources... [ 64%] api/generated/mdtraj.reporters.HDF5Reporter reading sources... [ 65%] api/generated/mdtraj.reporters.NetCDFReporter reading sources... [ 66%] api/generated/mdtraj.rmsd reading sources... [ 66%] api/generated/mdtraj.rmsf reading sources... [ 67%] api/generated/mdtraj.shrake_rupley reading sources... [ 68%] api/generated/mdtraj.static_dielectric reading sources... [ 69%] api/generated/mdtraj.thermal_expansion_alpha_P reading sources... [ 70%] api/generated/mdtraj.utils.box_vectors_to_lengths_and_angles reading sources... [ 70%] api/generated/mdtraj.utils.check_random_state reading sources... 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[ 82%] examples/atom-selection /usr/lib/python3/dist-packages/IPython/paths.py:66: UserWarning: IPython parent '/nonexistent/second-build' is not a writable location, using a temp directory. warn("IPython parent '{0}' is not a writable location," /usr/lib/python3/dist-packages/IPython/paths.py:66: UserWarning: IPython parent '/nonexistent/second-build' is not a writable location, using a temp directory. warn("IPython parent '{0}' is not a writable location," reading sources... [ 83%] examples/centroids /usr/lib/python3/dist-packages/IPython/paths.py:66: UserWarning: IPython parent '/nonexistent/second-build' is not a writable location, using a temp directory. warn("IPython parent '{0}' is not a writable location," /usr/lib/python3/dist-packages/IPython/paths.py:66: UserWarning: IPython parent '/nonexistent/second-build' is not a writable location, using a temp directory. warn("IPython parent '{0}' is not a writable location," reading sources... [ 84%] examples/clustering /usr/lib/python3/dist-packages/IPython/paths.py:66: UserWarning: IPython parent '/nonexistent/second-build' is not a writable location, using a temp directory. warn("IPython parent '{0}' is not a writable location," /usr/lib/python3/dist-packages/IPython/paths.py:66: UserWarning: IPython parent '/nonexistent/second-build' is not a writable location, using a temp directory. warn("IPython parent '{0}' is not a writable location," reading sources... [ 85%] examples/hbonds /usr/lib/python3/dist-packages/IPython/paths.py:66: UserWarning: IPython parent '/nonexistent/second-build' is not a writable location, using a temp directory. warn("IPython parent '{0}' is not a writable location," /usr/lib/python3/dist-packages/IPython/paths.py:66: UserWarning: IPython parent '/nonexistent/second-build' is not a writable location, using a temp directory. warn("IPython parent '{0}' is not a writable location," reading sources... [ 85%] examples/index reading sources... 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[ 88%] examples/native-contact /usr/lib/python3/dist-packages/IPython/paths.py:66: UserWarning: IPython parent '/nonexistent/second-build' is not a writable location, using a temp directory. warn("IPython parent '{0}' is not a writable location," /usr/lib/python3/dist-packages/IPython/paths.py:66: UserWarning: IPython parent '/nonexistent/second-build' is not a writable location, using a temp directory. warn("IPython parent '{0}' is not a writable location," reading sources... [ 88%] examples/nmr /usr/lib/python3/dist-packages/IPython/paths.py:66: UserWarning: IPython parent '/nonexistent/second-build' is not a writable location, using a temp directory. warn("IPython parent '{0}' is not a writable location," /usr/lib/python3/dist-packages/IPython/paths.py:66: UserWarning: IPython parent '/nonexistent/second-build' is not a writable location, using a temp directory. warn("IPython parent '{0}' is not a writable location," reading sources... 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[ 91%] examples/ramachandran-plot /usr/lib/python3/dist-packages/IPython/paths.py:66: UserWarning: IPython parent '/nonexistent/second-build' is not a writable location, using a temp directory. warn("IPython parent '{0}' is not a writable location," /usr/lib/python3/dist-packages/IPython/paths.py:66: UserWarning: IPython parent '/nonexistent/second-build' is not a writable location, using a temp directory. warn("IPython parent '{0}' is not a writable location," reading sources... [ 92%] examples/rmsd-benchmark /usr/lib/python3/dist-packages/IPython/paths.py:66: UserWarning: IPython parent '/nonexistent/second-build' is not a writable location, using a temp directory. warn("IPython parent '{0}' is not a writable location," /usr/lib/python3/dist-packages/IPython/paths.py:66: UserWarning: IPython parent '/nonexistent/second-build' is not a writable location, using a temp directory. warn("IPython parent '{0}' is not a writable location," reading sources... 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[100%] whatsnew /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/shape.py:docstring of mdtraj.geometry.shape.asphericity:9: WARNING: Block quote ends without a blank line; unexpected unindent. /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/contact.py:docstring of mdtraj.geometry.contact.compute_contacts:9: WARNING: Block quote ends without a blank line; unexpected unindent. /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/contact.py:docstring of mdtraj.geometry.contact.compute_contacts:36: WARNING: Unexpected indentation. /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/contact.py:docstring of mdtraj.geometry.contact.compute_contacts:45: WARNING: Block quote ends without a blank line; unexpected unindent. /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/contact.py:docstring of mdtraj.geometry.contact.compute_contacts:54: WARNING: Block quote ends without a blank line; unexpected unindent. docstring of mdtraj.formats.dtr.load_dtr:7: WARNING: Unexpected indentation. /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/shape.py:docstring of mdtraj.geometry.shape.relative_shape_antisotropy:9: WARNING: Block quote ends without a blank line; unexpected unindent. /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/rotation.py:docstring of mdtraj.utils.rotation.uniform_quaternion:32: WARNING: Error in "rubric" directive: no content permitted. .. rubric:: References .. [R17e8d31e726c-1] K. Shoemake. Uniform random rotations. In D. Kirk, editor, Graphics Gems III, pages 124-132. Academic, New York, 1992. .. [R17e8d31e726c-2] http://planning.cs.uiuc.edu/node198.html /build/reproducible-path/mdtraj-1.9.5/docs/installation.rst:1: WARNING: malformed hyperlink target. /build/reproducible-path/mdtraj-1.9.5/docs/mdconvert.rst:2: WARNING: Title underline too short. ``mdconvert`` (``mdconvert-mdtraj``) ============= looking for now-outdated files... none found pickling environment... done checking consistency... /build/reproducible-path/mdtraj-1.9.5/docs/building_docs.rst: WARNING: document isn't included in any toctree /build/reproducible-path/mdtraj-1.9.5/docs/faq.rst: WARNING: document isn't included in any toctree done preparing documents... done writing output... [ 0%] analysis writing output... [ 1%] api/generated/mdtraj.Topology writing output... [ 2%] api/generated/mdtraj.Trajectory writing output... 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[ 27%] api/generated/mdtraj.compute_rg writing output... [ 28%] api/generated/mdtraj.density writing output... [ 29%] api/generated/mdtraj.dipole_moments writing output... [ 29%] api/generated/mdtraj.formats.AmberNetCDFRestartFile writing output... [ 30%] api/generated/mdtraj.formats.AmberRestartFile writing output... [ 31%] api/generated/mdtraj.formats.ArcTrajectoryFile writing output... [ 32%] api/generated/mdtraj.formats.BINPOSTrajectoryFile writing output... [ 33%] api/generated/mdtraj.formats.DCDTrajectoryFile writing output... [ 33%] api/generated/mdtraj.formats.DTRTrajectoryFile writing output... [ 34%] api/generated/mdtraj.formats.GroTrajectoryFile writing output... [ 35%] api/generated/mdtraj.formats.HDF5TrajectoryFile writing output... [ 36%] api/generated/mdtraj.formats.LAMMPSTrajectoryFile writing output... [ 37%] api/generated/mdtraj.formats.LH5TrajectoryFile writing output... [ 37%] api/generated/mdtraj.formats.MDCRDTrajectoryFile writing output... [ 38%] api/generated/mdtraj.formats.NetCDFTrajectoryFile writing output... [ 39%] api/generated/mdtraj.formats.PDBTrajectoryFile writing output... [ 40%] api/generated/mdtraj.formats.TRRTrajectoryFile writing output... [ 40%] api/generated/mdtraj.formats.XTCTrajectoryFile writing output... [ 41%] api/generated/mdtraj.formats.XYZTrajectoryFile writing output... [ 42%] api/generated/mdtraj.geometry.squareform writing output... [ 43%] api/generated/mdtraj.isothermal_compressability_kappa_T writing output... [ 44%] api/generated/mdtraj.iterload writing output... [ 44%] api/generated/mdtraj.join writing output... [ 45%] api/generated/mdtraj.kabsch_sander writing output... [ 46%] api/generated/mdtraj.load writing output... [ 47%] api/generated/mdtraj.load_arc writing output... [ 48%] api/generated/mdtraj.load_binpos writing output... [ 48%] api/generated/mdtraj.load_dcd writing output... [ 49%] api/generated/mdtraj.load_dtr writing output... [ 50%] api/generated/mdtraj.load_frame writing output... [ 51%] api/generated/mdtraj.load_hdf5 writing output... [ 51%] api/generated/mdtraj.load_hoomdxml writing output... [ 52%] api/generated/mdtraj.load_lammpstrj writing output... [ 53%] api/generated/mdtraj.load_lh5 writing output... [ 54%] api/generated/mdtraj.load_netcdf writing output... [ 55%] api/generated/mdtraj.load_pdb writing output... [ 55%] api/generated/mdtraj.load_prmtop writing output... [ 56%] api/generated/mdtraj.load_trr writing output... [ 57%] api/generated/mdtraj.load_xml writing output... [ 58%] api/generated/mdtraj.load_xtc writing output... [ 59%] api/generated/mdtraj.load_xyz writing output... [ 59%] api/generated/mdtraj.lprmsd writing output... [ 60%] api/generated/mdtraj.open writing output... [ 61%] api/generated/mdtraj.principal_moments writing output... [ 62%] api/generated/mdtraj.reindex_dataframe_by_atoms writing output... [ 62%] api/generated/mdtraj.relative_shape_antisotropy writing output... [ 63%] api/generated/mdtraj.reporters.DCDReporter writing output... [ 64%] api/generated/mdtraj.reporters.HDF5Reporter writing output... [ 65%] api/generated/mdtraj.reporters.NetCDFReporter writing output... [ 66%] api/generated/mdtraj.rmsd writing output... [ 66%] api/generated/mdtraj.rmsf writing output... [ 67%] api/generated/mdtraj.shrake_rupley writing output... [ 68%] api/generated/mdtraj.static_dielectric writing output... [ 69%] api/generated/mdtraj.thermal_expansion_alpha_P writing output... [ 70%] api/generated/mdtraj.utils.box_vectors_to_lengths_and_angles writing output... [ 70%] api/generated/mdtraj.utils.check_random_state writing output... [ 71%] api/generated/mdtraj.utils.ensure_type writing output... [ 72%] api/generated/mdtraj.utils.ilen writing output... [ 73%] api/generated/mdtraj.utils.import_ writing output... [ 74%] api/generated/mdtraj.utils.in_units_of writing output... [ 74%] api/generated/mdtraj.utils.lengths_and_angles_to_box_vectors writing output... [ 75%] api/generated/mdtraj.utils.rotation_matrix_from_quaternion writing output... [ 76%] api/generated/mdtraj.utils.timing writing output... [ 77%] api/generated/mdtraj.utils.uniform_quaternion writing output... [ 77%] api/generated/mdtraj.wernet_nilsson writing output... [ 78%] api/reporters writing output... [ 79%] api/trajectory_files writing output... [ 80%] api/utils writing output... [ 81%] atom_selection writing output... [ 81%] building_docs writing output... [ 82%] examples/atom-selection writing output... [ 83%] examples/centroids writing output... [ 84%] examples/clustering writing output... [ 85%] examples/hbonds writing output... [ 85%] examples/index writing output... [ 86%] examples/introduction writing output... [ 87%] examples/iterload writing output... [ 88%] examples/native-contact writing output... [ 88%] examples/nmr writing output... [ 89%] examples/openmm writing output... [ 90%] examples/pca writing output... [ 91%] examples/ramachandran-plot writing output... [ 92%] examples/rmsd-benchmark writing output... [ 92%] examples/solvent-accessible-surface-area writing output... [ 93%] examples/two-pass-clustering writing output... [ 94%] faq writing output... [ 95%] hdf5_format writing output... [ 96%] index writing output... [ 96%] installation writing output... [ 97%] load_functions writing output... [ 98%] mdconvert writing output... [ 99%] new_to_python writing output... [100%] whatsnew generating indices... genindex done writing additional pages... search done copying static files... done copying extra files... done dumping search index in English (code: en)... done dumping object inventory... done build succeeded, 12 warnings. The HTML pages are in ../build/html. Build finished. The HTML pages are in /build/reproducible-path/mdtraj-1.9.5/build/html. make[2]: Leaving directory '/build/reproducible-path/mdtraj-1.9.5/docs' for img in `find /build/reproducible-path/mdtraj-1.9.5/build/html/examples -name *.png`; do \ mv $img /build/reproducible-path/mdtraj-1.9.5/build/html/examples; \ done sed "s|/build/reproducible-path/mdtraj-1.9.5/build/html/examples/|./|g; s|.ipynb|.ipynb.gz|g" -i /build/reproducible-path/mdtraj-1.9.5/build/html/examples/*.html sed "s|/build/reproducible-path/mdtraj-1.9.5/debian/external|http://www.rcsb.org/pdb/files|g" -i /build/reproducible-path/mdtraj-1.9.5/build/html/examples/*.html /build/reproducible-path/mdtraj-1.9.5/build/html/examples/*/*.*py* rm /build/reproducible-path/mdtraj-1.9.5/build/html/examples/iterload/data rm -rf /build/reproducible-path/mdtraj-1.9.5/examples mv /build/reproducible-path/mdtraj-1.9.5/examples.orig /build/reproducible-path/mdtraj-1.9.5/examples make[1]: Leaving directory '/build/reproducible-path/mdtraj-1.9.5' dh_auto_build -O--buildsystem=pybuild -Npython-mdtraj-doc I: pybuild base:232: /usr/bin/python3 setup.py build Using built-in specs. COLLECT_GCC=/usr/bin/x86_64-linux-gnu-gcc COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/10/lto-wrapper OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa:hsa OFFLOAD_TARGET_DEFAULT=1 Target: x86_64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 10.2.1-6' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/gcc-10-Km9U7s/gcc-10-10.2.1/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-10-Km9U7s/gcc-10-10.2.1/debian/tmp-gcn/usr,hsa --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-mutex Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 10.2.1 20210110 (Debian 10.2.1-6) C compiler: Attempting to autodetect OpenMP support... Compiler supports OpenMP Attempting to autodetect SSE3 support... Compiler supports SSE3 Attempting to autodetect SSE4.1 support... Compiler supports SSE4.1 Attempting to autodetect NEON support... Did not detect NEON support running build running build_py copying mdtraj/version.py -> /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj running build_ext dh_auto_test -O--buildsystem=pybuild I: pybuild base:232: cd /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build; python3.9 -m unittest discover -v ---------------------------------------------------------------------- Ran 0 tests in 0.001s OK create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary --with python3,sphinxdoc --buildsystem=pybuild dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_installdirs -O--buildsystem=pybuild dh_auto_install -O--buildsystem=pybuild I: pybuild base:232: /usr/bin/python3 setup.py install --root /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj Using built-in specs. COLLECT_GCC=/usr/bin/x86_64-linux-gnu-gcc COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/10/lto-wrapper OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa:hsa OFFLOAD_TARGET_DEFAULT=1 Target: x86_64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 10.2.1-6' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/gcc-10-Km9U7s/gcc-10-10.2.1/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-10-Km9U7s/gcc-10-10.2.1/debian/tmp-gcn/usr,hsa --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-mutex Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 10.2.1 20210110 (Debian 10.2.1-6) C compiler: Attempting to autodetect OpenMP support... Compiler supports OpenMP Attempting to autodetect SSE3 support... Compiler supports SSE3 Attempting to autodetect SSE4.1 support... Compiler supports SSE4.1 Attempting to autodetect NEON support... Did not detect NEON support running install running build running build_py copying mdtraj/version.py -> /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj running build_ext running install_lib creating /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj creating /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr creating /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib creating /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9 creating /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages creating /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/version.py -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj creating /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/__pycache__ copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/__pycache__/version.cpython-39.pyc -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/__pycache__ copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/__pycache__/__init__.cpython-39.pyc -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/__pycache__ copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/_lprmsd.cpython-39-x86_64-linux-gnu.so -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/_rmsd.cpython-39-x86_64-linux-gnu.so -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj creating /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/core creating /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/core/__pycache__ copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/core/__pycache__/trajectory.cpython-39.pyc -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/core/__pycache__ copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/core/__pycache__/selection.cpython-39.pyc -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/core/__pycache__ copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/core/__pycache__/residue_names.cpython-39.pyc -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/core/__pycache__ copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/core/__pycache__/topology.cpython-39.pyc -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/core/__pycache__ copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/core/__pycache__/element.cpython-39.pyc -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/core/__pycache__ copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/core/__pycache__/__init__.cpython-39.pyc -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/core/__pycache__ creating /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/core/lib copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/core/lib/center.h -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/core/lib copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/core/lib/theobald_rmsd.h -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/core/lib copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/core/lib/libtheobald.a -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/core/lib copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/core/__init__.py -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/core copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/core/element.py -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/core copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/core/residue_names.py -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/core copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/core/topology.py -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/core copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/core/trajectory.py -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/core copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/core/selection.py -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/core creating /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats creating /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/__pycache__/gsd.cpython-39.pyc -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/__pycache__/hoomdxml.cpython-39.pyc -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/__pycache__/mol2.cpython-39.pyc -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/__pycache__/psf.cpython-39.pyc -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/__pycache__/prmtop.cpython-39.pyc -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/__pycache__/openmmxml.cpython-39.pyc -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/__pycache__/xyzfile.cpython-39.pyc -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/__pycache__/gro.cpython-39.pyc -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/__pycache__/lammpstrj.cpython-39.pyc -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/__pycache__/amberrst.cpython-39.pyc -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/__pycache__/mdcrd.cpython-39.pyc -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/__pycache__/lh5.cpython-39.pyc -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/__pycache__/netcdf.cpython-39.pyc -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/__pycache__/hdf5.cpython-39.pyc -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/__pycache__/registry.cpython-39.pyc -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/__pycache__/arc.cpython-39.pyc -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/__pycache__/__init__.cpython-39.pyc -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/dtr.cpython-39-x86_64-linux-gnu.so -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/binpos.cpython-39-x86_64-linux-gnu.so -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/dcd.cpython-39-x86_64-linux-gnu.so -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/tng.cpython-39-x86_64-linux-gnu.so -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/trr.cpython-39-x86_64-linux-gnu.so -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/xtc.cpython-39-x86_64-linux-gnu.so -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats creating /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/pdb creating /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/pdb/__pycache__ copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/pdb/__pycache__/pdbstructure.cpython-39.pyc -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/pdb/__pycache__ copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/pdb/__pycache__/pdbfile.cpython-39.pyc -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/pdb/__pycache__ copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/pdb/__pycache__/__init__.cpython-39.pyc -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/pdb/__pycache__ creating /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/pdb/data copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/pdb/data/pdbNames.xml -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/pdb/data copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/pdb/data/residues.xml -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/pdb/data copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/pdb/__init__.py -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/pdb copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/pdb/pdbfile.py -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/pdb copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/pdb/pdbstructure.py -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/pdb copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/__init__.py -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/amberrst.py -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/arc.py -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/gro.py -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/gsd.py -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/hdf5.py -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/hoomdxml.py -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/lammpstrj.py -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/lh5.py -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/mdcrd.py -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/mol2.py -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/netcdf.py -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/openmmxml.py -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/prmtop.py -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/psf.py -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/registry.py -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/xyzfile.py -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats creating /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry creating /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/__pycache__/alignment.cpython-39.pyc -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/__pycache__/shape.cpython-39.pyc -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/__pycache__/order.cpython-39.pyc -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/__pycache__/rdf.cpython-39.pyc -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/__pycache__/thermodynamic_properties.cpython-39.pyc -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/__pycache__/dssp.cpython-39.pyc -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/__pycache__/contact.cpython-39.pyc -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/__pycache__/sasa.cpython-39.pyc -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/__pycache__/hbond.cpython-39.pyc -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/__pycache__/dihedral.cpython-39.pyc -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/__pycache__/distance.cpython-39.pyc -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/__pycache__/angle.cpython-39.pyc -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/__pycache__/rg.cpython-39.pyc -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/__pycache__/__init__.cpython-39.pyc -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/neighborlist.cpython-39-x86_64-linux-gnu.so -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/neighbors.cpython-39-x86_64-linux-gnu.so -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/drid.cpython-39-x86_64-linux-gnu.so -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/_geometry.cpython-39-x86_64-linux-gnu.so -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/__init__.py -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/alignment.py -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/angle.py -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/contact.py -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/dihedral.py -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/distance.py -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/dssp.py -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/hbond.py -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/internal.py -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/order.py -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/rdf.py -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/rg.py -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/sasa.py -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/shape.py -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/thermodynamic_properties.py -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry creating /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/nmr creating /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/nmr/__pycache__ copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/nmr/__pycache__/scalar_couplings.cpython-39.pyc -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/nmr/__pycache__ copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/nmr/__pycache__/shift_wrappers.cpython-39.pyc -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/nmr/__pycache__ copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/nmr/__pycache__/__init__.cpython-39.pyc -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/nmr/__pycache__ copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/nmr/__init__.py -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/nmr copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/nmr/scalar_couplings.py -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/nmr copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/nmr/shift_wrappers.py -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/nmr creating /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/reporters creating /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/reporters/__pycache__ copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/reporters/__pycache__/xtcreporter.cpython-39.pyc -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/reporters/__pycache__ copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/reporters/__pycache__/dcdreporter.cpython-39.pyc -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/reporters/__pycache__ copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/reporters/__pycache__/netcdfreporter.cpython-39.pyc -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/reporters/__pycache__ copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/reporters/__pycache__/basereporter.cpython-39.pyc -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/reporters/__pycache__ copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/reporters/__pycache__/hdf5reporter.cpython-39.pyc -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/reporters/__pycache__ copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/reporters/__pycache__/__init__.cpython-39.pyc -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/reporters/__pycache__ copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/reporters/__init__.py -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/reporters copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/reporters/basereporter.py -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/reporters copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/reporters/dcdreporter.py -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/reporters copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/reporters/hdf5reporter.py -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/reporters copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/reporters/netcdfreporter.py -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/reporters copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/reporters/xtcreporter.py -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/reporters creating /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/scripts creating /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/scripts/__pycache__ copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/scripts/__pycache__/__init__.cpython-39.pyc -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/scripts/__pycache__ copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/scripts/__init__.py -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/scripts copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/scripts/mdconvert.py -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/scripts copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/scripts/mdinspect.py -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/scripts creating /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/testing creating /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/testing/__pycache__ copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/testing/__pycache__/docscrape.cpython-39.pyc -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/testing/__pycache__ copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/testing/__pycache__/docstrings.cpython-39.pyc -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/testing/__pycache__ copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/testing/__pycache__/testing.cpython-39.pyc -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/testing/__pycache__ copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/testing/__pycache__/__init__.cpython-39.pyc -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/testing/__pycache__ copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/testing/__init__.py -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/testing copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/testing/docscrape.py -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/testing copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/testing/docstrings.py -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/testing copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/testing/testing.py -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/testing creating /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils creating /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/__pycache__/singleton.cpython-39.pyc -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/__pycache__/zipped.cpython-39.pyc -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/__pycache__/contextmanagers.cpython-39.pyc -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/__pycache__/unitcell.cpython-39.pyc -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/__pycache__/rotation.cpython-39.pyc -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/__pycache__/six.cpython-39.pyc -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/__pycache__/validation.cpython-39.pyc -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/__pycache__/delay_import.cpython-39.pyc -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/__pycache__/__init__.cpython-39.pyc -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/__pycache__ creating /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit creating /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit/__pycache__/prefix.cpython-39.pyc -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit/__pycache__/unit_operators.cpython-39.pyc -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit/__pycache__/unit_definitions.cpython-39.pyc -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit/__pycache__/baseunit.cpython-39.pyc -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit/__pycache__/mymatrix.cpython-39.pyc -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit/__pycache__/unit.cpython-39.pyc -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit/__pycache__/basedimension.cpython-39.pyc -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit/__pycache__/standard_dimensions.cpython-39.pyc -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit/__pycache__/quantity.cpython-39.pyc -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit/__pycache__/__init__.cpython-39.pyc -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit/__init__.py -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit/basedimension.py -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit/baseunit.py -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit/doctests.py -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit/mymatrix.py -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit/unit.py -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit/constants.py -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit/prefix.py -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit/quantity.py -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit/standard_dimensions.py -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit/unit_definitions.py -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit/unit_math.py -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit/unit_operators.py -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/__init__.py -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/contextmanagers.py -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/delay_import.py -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/rotation.py -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/singleton.py -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/six.py -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unitcell.py -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/validation.py -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/zipped.py -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/__init__.py -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj copying /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/io.py -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj byte-compiling /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/version.py to version.cpython-39.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/core/__init__.py to __init__.cpython-39.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/core/element.py to element.cpython-39.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/core/residue_names.py to residue_names.cpython-39.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/core/topology.py to topology.cpython-39.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/core/trajectory.py to trajectory.cpython-39.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/core/selection.py to selection.cpython-39.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/pdb/__init__.py to __init__.cpython-39.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/pdb/pdbfile.py to pdbfile.cpython-39.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/pdb/pdbstructure.py to pdbstructure.cpython-39.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/__init__.py to __init__.cpython-39.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/amberrst.py to amberrst.cpython-39.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/arc.py to arc.cpython-39.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/gro.py to gro.cpython-39.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/gsd.py to gsd.cpython-39.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/hdf5.py to hdf5.cpython-39.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/hoomdxml.py to hoomdxml.cpython-39.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/lammpstrj.py to lammpstrj.cpython-39.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/lh5.py to lh5.cpython-39.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/mdcrd.py to mdcrd.cpython-39.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/mol2.py to mol2.cpython-39.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/netcdf.py to netcdf.cpython-39.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/openmmxml.py to openmmxml.cpython-39.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/prmtop.py to prmtop.cpython-39.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/psf.py to psf.cpython-39.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/registry.py to registry.cpython-39.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/xyzfile.py to xyzfile.cpython-39.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry/__init__.py to __init__.cpython-39.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry/alignment.py to alignment.cpython-39.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry/angle.py to angle.cpython-39.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry/contact.py to contact.cpython-39.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry/dihedral.py to dihedral.cpython-39.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry/distance.py to distance.cpython-39.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry/dssp.py to dssp.cpython-39.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry/hbond.py to hbond.cpython-39.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry/internal.py to internal.cpython-39.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry/order.py to order.cpython-39.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry/rdf.py to rdf.cpython-39.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry/rg.py to rg.cpython-39.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry/sasa.py to sasa.cpython-39.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry/shape.py to shape.cpython-39.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry/thermodynamic_properties.py to thermodynamic_properties.cpython-39.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/nmr/__init__.py to __init__.cpython-39.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/nmr/scalar_couplings.py to scalar_couplings.cpython-39.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/nmr/shift_wrappers.py to shift_wrappers.cpython-39.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/reporters/__init__.py to __init__.cpython-39.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/reporters/basereporter.py to basereporter.cpython-39.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/reporters/dcdreporter.py to dcdreporter.cpython-39.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/reporters/hdf5reporter.py to hdf5reporter.cpython-39.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/reporters/netcdfreporter.py to netcdfreporter.cpython-39.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/reporters/xtcreporter.py to xtcreporter.cpython-39.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/scripts/__init__.py to __init__.cpython-39.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/scripts/mdconvert.py to mdconvert.cpython-39.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/scripts/mdinspect.py to mdinspect.cpython-39.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/testing/__init__.py to __init__.cpython-39.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/testing/docscrape.py to docscrape.cpython-39.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/testing/docstrings.py to docstrings.cpython-39.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/testing/testing.py to testing.cpython-39.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit/__init__.py to __init__.cpython-39.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit/basedimension.py to basedimension.cpython-39.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit/baseunit.py to baseunit.cpython-39.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit/doctests.py to doctests.cpython-39.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit/mymatrix.py to mymatrix.cpython-39.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit/unit.py to unit.cpython-39.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit/constants.py to constants.cpython-39.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit/prefix.py to prefix.cpython-39.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit/quantity.py to quantity.cpython-39.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit/standard_dimensions.py to standard_dimensions.cpython-39.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit/unit_definitions.py to unit_definitions.cpython-39.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit/unit_math.py to unit_math.cpython-39.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit/unit_operators.py to unit_operators.cpython-39.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/__init__.py to __init__.cpython-39.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/contextmanagers.py to contextmanagers.cpython-39.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/delay_import.py to delay_import.cpython-39.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/rotation.py to rotation.cpython-39.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/singleton.py to singleton.cpython-39.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/six.py to six.cpython-39.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unitcell.py to unitcell.cpython-39.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/validation.py to validation.cpython-39.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/zipped.py to zipped.cpython-39.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/__init__.py to __init__.cpython-39.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/io.py to io.cpython-39.pyc running install_egg_info running egg_info creating mdtraj.egg-info writing mdtraj.egg-info/PKG-INFO writing dependency_links to mdtraj.egg-info/dependency_links.txt writing entry points to mdtraj.egg-info/entry_points.txt writing requirements to mdtraj.egg-info/requires.txt writing top-level names to mdtraj.egg-info/top_level.txt writing manifest file 'mdtraj.egg-info/SOURCES.txt' reading manifest file 'mdtraj.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' no previously-included directories found matching '__pycache__' no previously-included directories found matching '*.pyc' writing manifest file 'mdtraj.egg-info/SOURCES.txt' Copying mdtraj.egg-info to /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj-1.9.5.egg-info Skipping SOURCES.txt running install_scripts Installing mdconvert-mdtraj script to /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/bin Installing mdinspect script to /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/bin dh_install -O--buildsystem=pybuild dh_installdocs -O--buildsystem=pybuild dh_installdocs: warning: Cannot auto-detect main package for python-mdtraj-doc. If the default is wrong, please use --doc-main-package debian/rules override_dh_sphinxdoc-indep make[1]: Entering directory '/build/reproducible-path/mdtraj-1.9.5' dh_sphinxdoc -i dh_sphinxdoc: warning: ignoring unknown JavaScript code: debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/js/versions.js grep "https://cdnjs.cloudflare.com/ajax/libs/mathjax/.*/latest.js" debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/* -r --files-with-matches | xargs sed "s|src=\"https://cdnjs.cloudflare.com/ajax/libs/mathjax/.*/latest.js|src=\"file://usr/share/javascript/mathjax/unpacked/latest.js|g" -i sed "s|src=\"https://img.shields.io/badge/DOI-10.1016%2Fj.bpj.2015.08.015-blue.svg\"|src=\"_static/doi-10.1016_j.bpj.2015.08.015-blue.svg\"|g" -i debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/index.html make[1]: Leaving directory '/build/reproducible-path/mdtraj-1.9.5' dh_sphinxdoc -O--buildsystem=pybuild -Npython-mdtraj-doc dh_sphinxdoc: warning: Sphinx documentation not found dh_installchangelogs -O--buildsystem=pybuild dh_installexamples -O--buildsystem=pybuild dh_installexamples: warning: Cannot auto-detect main package for python-mdtraj-doc. If the default is wrong, please use --doc-main-package dh_installman -O--buildsystem=pybuild dh_python3 -O--buildsystem=pybuild dh_installsystemduser -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild dh_compress -O--buildsystem=pybuild dh_fixperms -O--buildsystem=pybuild dh_missing -O--buildsystem=pybuild dh_dwz -a -O--buildsystem=pybuild dh_strip -a -O--buildsystem=pybuild dh_makeshlibs -a -O--buildsystem=pybuild dh_shlibdeps -a -O--buildsystem=pybuild dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dpkg-gencontrol: warning: package python3-mdtraj: substitution variable ${python3:Provides} unused, but is defined dpkg-gencontrol: warning: package python3-mdtraj: substitution variable ${python3:Versions} unused, but is defined dpkg-gencontrol: warning: package python3-mdtraj: substitution variable ${python3:Provides} unused, but is defined dpkg-gencontrol: warning: package python3-mdtraj: substitution variable ${python3:Versions} unused, but is defined dpkg-gencontrol: warning: package python-mdtraj-doc: substitution variable ${sphinxdoc:Built-Using} unused, but is defined dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'python3-mdtraj-dbgsym' in '../python3-mdtraj-dbgsym_1.9.5-1_amd64.deb'. dpkg-deb: building package 'python-mdtraj-doc' in '../python-mdtraj-doc_1.9.5-1_all.deb'. dpkg-deb: building package 'python3-mdtraj' in '../python3-mdtraj_1.9.5-1_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../mdtraj_1.9.5-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-source: info: using options from mdtraj-1.9.5/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/4100091/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/4100091/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/4100091 and its subdirectories I: Current time: Sun Jan 7 04:18:56 +14 2024 I: pbuilder-time-stamp: 1704550736