Sat Jan 6 22:40:28 UTC 2024 I: starting to build mdtraj/bullseye/i386 on jenkins on '2024-01-06 22:40' Sat Jan 6 22:40:28 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_8/13875/console.log Sat Jan 6 22:40:28 UTC 2024 I: Downloading source for bullseye/mdtraj=1.9.5-1 --2024-01-06 22:40:28-- http://cdn-fastly.deb.debian.org/debian/pool/main/m/mdtraj/mdtraj_1.9.5-1.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2592 (2.5K) [text/prs.lines.tag] Saving to: ‘mdtraj_1.9.5-1.dsc’ 0K .. 100% 178M=0s 2024-01-06 22:40:28 (178 MB/s) - ‘mdtraj_1.9.5-1.dsc’ saved [2592/2592] Sat Jan 6 22:40:28 UTC 2024 I: mdtraj_1.9.5-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: mdtraj Binary: python3-mdtraj, python-mdtraj-doc Architecture: any-amd64 arm64 i386 all Version: 1.9.5-1 Maintainer: Debichem Team Uploaders: Drew Parsons Homepage: http://mdtraj.org/ Standards-Version: 4.5.1 Vcs-Browser: https://salsa.debian.org/debichem-team/mdtraj Vcs-Git: https://salsa.debian.org/debichem-team/mdtraj.git Testsuite: autopkgtest Testsuite-Triggers: python3-ipykernel, python3-jupyter-client, python3-matplotlib, python3-nbformat, python3-pandas, python3-pytest, python3-six, python3-sklearn Build-Depends: debhelper-compat (= 13), dh-python, cython3 (>= 0.29~), python3-setuptools, python3-all-dev, python3-numpy (>= 1.6~), python3-scipy, python3-astor, python3-networkx, python3-pandas, python3-pyparsing, python3-sphinx, python3-tables, libjs-mathjax Build-Depends-Indep: python3-msmb-theme, python3-ipykernel, python3-jupyter-client, python3-matplotlib, python3-nbconvert, python3-nbformat, python3-numpydoc, python3-six, python3-sklearn Package-List: python-mdtraj-doc deb doc optional arch=all python3-mdtraj deb python optional arch=any-amd64,arm64,i386 Checksums-Sha1: 7db579a63370fc047be4b3ffa4f2d7e74cb3a27f 21487803 mdtraj_1.9.5.orig.tar.gz 88c8d5fc681a4c509bf82d260c6544da5f68c5dc 295596 mdtraj_1.9.5-1.debian.tar.xz Checksums-Sha256: ed2a72b85e765024f8d533da26dad026944d0e385b04af7b66572f676ef92040 21487803 mdtraj_1.9.5.orig.tar.gz df92f102aa175ce4ba689f4486d7c8fb15e46e3efed8ae2b436351df1854ac2e 295596 mdtraj_1.9.5-1.debian.tar.xz Files: 74ffbce786aa7524e99bee9d95462701 21487803 mdtraj_1.9.5.orig.tar.gz ed728d470689c78f5f7013453cf31451 295596 mdtraj_1.9.5-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCAAdFiEEI8mpPlhYGekSbQo2Vz7x5L1aAfoFAmAFIaQACgkQVz7x5L1a Afo0Bg//SipOUq6kj0mtyTvbfLrnRLyVlyOLW13Gh2dbGuJLsmqFKLKd/IxeauNs b0ZOcyjuISoI8bDBp77ow+HPHT12+fmT8iQZwKtXt5cUuzomRqwWyOnSEb6xzLdn ZNjf4iVQsWdy7ZVuJ9xyEXg5PjOOJQJjstEqwjxnlXjvdVfjWO37WCc1HRU2krIm uKAc0c0jLFt6lHEei5n0zLJvhuKjj1wLtrXe8DKEE48Lib0+9bMGCB5Sxi6+tMU6 Wr/RX9bGt5mt0xnuHlsDiqlwnkLL1BPFOG4Es9KuFuphcyDlq178LsX6sFmpbB4N E/wfx5B2GjzpfGAxVVjb0+wFbSDT83PO+txQTjUcItQ+kbtdDegPywR5zjHwIoIG x9z996S1Tqe2sYOSMObmRfb9wyzFUx1K7NRI1ThqREXeoZ/lVs+uFPiySClS2sdf zwNtpN7aZWvVTFWJdHk9tdXqRV8CtHAdpgmnoTkM/LOijEBOhwwBNLb2dX22zIZC H+EYf22dMv6CQ0w1vNVkNuJhBVNdQJTK3do+gnwTkDUtHSnVsX9a20xk8a0LTVnr 3kmg/KwyUy2jOQOpmhlJshj17k2/LEpjujELS6r+Q4ymf1i0xtlDqs0e3gvLzfvh Sn6kifcd0xRzC/8vAVe2/WmTfaPzL4+ALo6akBuT1c8JV4VO0/w= =Ee7h -----END PGP SIGNATURE----- Sat Jan 6 22:40:28 UTC 2024 I: Checking whether the package is not for us Sat Jan 6 22:40:28 UTC 2024 I: Starting 1st build on remote node ionos16-i386.debian.net. Sat Jan 6 22:40:28 UTC 2024 I: Preparing to do remote build '1' on ionos16-i386.debian.net. Sat Jan 6 22:47:39 UTC 2024 I: Deleting $TMPDIR on ionos16-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Fri Feb 7 17:03:30 -12 2025 I: pbuilder-time-stamp: 1738991010 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: using eatmydata during job 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.2nnIm_tO/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/104979/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='i386' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=16 ' DISTRIBUTION='bullseye' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='3d9715272a734ed28896268b70e76957' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' LD_LIBRARY_PATH='/usr/lib/libeatmydata' LD_PRELOAD='libeatmydata.so' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='104979' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.UfSHoaZj/pbuilderrc_9I8K --distribution bullseye --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.UfSHoaZj/b1 --logfile b1/build.log mdtraj_1.9.5-1.dsc' SUDO_GID='112' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://85.184.249.68:3128' I: uname -a Linux ionos16-i386 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 5776 -rwxr-xr-x 1 root root 1367848 Mar 27 2022 bash -rwxr-xr-x 3 root root 38280 Jul 20 2020 bunzip2 -rwxr-xr-x 3 root root 38280 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 38280 Jul 20 2020 bzip2 -rwxr-xr-x 1 root root 17768 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 38824 Sep 22 2020 cat -rwxr-xr-x 1 root root 71624 Sep 22 2020 chgrp -rwxr-xr-x 1 root root 67528 Sep 22 2020 chmod -rwxr-xr-x 1 root root 75752 Sep 22 2020 chown -rwxr-xr-x 1 root root 157960 Sep 22 2020 cp -rwxr-xr-x 1 root root 128724 Dec 10 2020 dash -rwxr-xr-x 1 root root 124904 Sep 22 2020 date -rwxr-xr-x 1 root root 92172 Sep 22 2020 dd -rwxr-xr-x 1 root root 100752 Sep 22 2020 df -rwxr-xr-x 1 root root 153964 Sep 22 2020 dir -rwxr-xr-x 1 root root 83644 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 34664 Sep 22 2020 echo -rwxr-xr-x 1 root root 28 Jan 25 2023 egrep -rwxr-xr-x 1 root root 34664 Sep 22 2020 false -rwxr-xr-x 1 root root 28 Jan 25 2023 fgrep -rwxr-xr-x 1 root root 71928 Jan 20 2022 findmnt -rwsr-xr-x 1 root root 30112 Feb 26 2021 fusermount -rwxr-xr-x 1 root root 210488 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 100952 Apr 10 2022 gzip -rwxr-xr-x 1 root root 21916 Nov 7 2019 hostname -rwxr-xr-x 1 root root 83980 Sep 22 2020 ln -rwxr-xr-x 1 root root 55572 Feb 7 2020 login -rwxr-xr-x 1 root root 153964 Sep 22 2020 ls -rwxr-xr-x 1 root root 153124 Jan 20 2022 lsblk -rwxr-xr-x 1 root root 96328 Sep 22 2020 mkdir -rwxr-xr-x 1 root root 79912 Sep 22 2020 mknod -rwxr-xr-x 1 root root 47048 Sep 22 2020 mktemp -rwxr-xr-x 1 root root 58920 Jan 20 2022 more -rwsr-xr-x 1 root root 50720 Jan 20 2022 mount -rwxr-xr-x 1 root root 13856 Jan 20 2022 mountpoint -rwxr-xr-x 1 root root 157996 Sep 22 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 38824 Sep 22 2020 pwd lrwxrwxrwx 1 root root 4 Mar 27 2022 rbash -> bash -rwxr-xr-x 1 root root 46984 Sep 22 2020 readlink -rwxr-xr-x 1 root root 75720 Sep 22 2020 rm -rwxr-xr-x 1 root root 46984 Sep 22 2020 rmdir -rwxr-xr-x 1 root root 22292 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 125036 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Jan 8 15:47 sh -> dash -rwxr-xr-x 1 root root 34696 Sep 22 2020 sleep -rwxr-xr-x 1 root root 83880 Sep 22 2020 stty -rwsr-xr-x 1 root root 79396 Jan 20 2022 su -rwxr-xr-x 1 root root 34696 Sep 22 2020 sync -rwxr-xr-x 1 root root 602584 Feb 17 2021 tar -rwxr-xr-x 1 root root 13860 Sep 27 2020 tempfile -rwxr-xr-x 1 root root 108520 Sep 22 2020 touch -rwxr-xr-x 1 root root 34664 Sep 22 2020 true -rwxr-xr-x 1 root root 17768 Feb 26 2021 ulockmgr_server -rwsr-xr-x 1 root root 30236 Jan 20 2022 umount -rwxr-xr-x 1 root root 34664 Sep 22 2020 uname -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress -rwxr-xr-x 1 root root 153964 Sep 22 2020 vdir -rwxr-xr-x 1 root root 63024 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/104979/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: i386 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 ... 17763 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-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 103 MB of archives. After unpacking 446 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main i386 bsdextrautils i386 2.36.1-8+deb11u1 [149 kB] Get: 2 http://deb.debian.org/debian bullseye/main i386 libuchardet0 i386 0.0.7-1 [67.9 kB] Get: 3 http://deb.debian.org/debian bullseye/main i386 groff-base i386 1.22.4-6 [952 kB] Get: 4 http://deb.debian.org/debian bullseye/main i386 libpipeline1 i386 1.5.3-1 [36.8 kB] Get: 5 http://deb.debian.org/debian bullseye/main i386 man-db i386 2.9.4-2 [1367 kB] Get: 6 http://deb.debian.org/debian bullseye/main i386 fonts-lato all 2.0-2.1 [2696 kB] Get: 7 http://deb.debian.org/debian bullseye/main i386 libpython3.9-minimal i386 3.9.2-1 [801 kB] Get: 8 http://deb.debian.org/debian bullseye/main i386 libexpat1 i386 2.2.10-2+deb11u5 [101 kB] Get: 9 http://deb.debian.org/debian bullseye/main i386 python3.9-minimal i386 3.9.2-1 [1956 kB] Get: 10 http://deb.debian.org/debian bullseye/main i386 python3-minimal i386 3.9.2-3 [38.2 kB] Get: 11 http://deb.debian.org/debian bullseye/main i386 media-types all 4.0.0 [30.3 kB] Get: 12 http://deb.debian.org/debian bullseye/main i386 mailcap all 3.69 [31.7 kB] Get: 13 http://deb.debian.org/debian bullseye/main i386 mime-support all 3.66 [10.9 kB] Get: 14 http://deb.debian.org/debian bullseye/main i386 tzdata all 2021a-1+deb11u10 [286 kB] Get: 15 http://deb.debian.org/debian bullseye/main i386 libmpdec3 i386 2.5.1-1 [91.9 kB] Get: 16 http://deb.debian.org/debian bullseye/main i386 readline-common all 8.1-1 [73.7 kB] Get: 17 http://deb.debian.org/debian bullseye/main i386 libreadline8 i386 8.1-1 [173 kB] Get: 18 http://deb.debian.org/debian bullseye/main i386 libpython3.9-stdlib i386 3.9.2-1 [1703 kB] Get: 19 http://deb.debian.org/debian bullseye/main i386 python3.9 i386 3.9.2-1 [466 kB] Get: 20 http://deb.debian.org/debian bullseye/main i386 libpython3-stdlib i386 3.9.2-3 [21.4 kB] Get: 21 http://deb.debian.org/debian bullseye/main i386 python3 i386 3.9.2-3 [37.9 kB] Get: 22 http://deb.debian.org/debian bullseye/main i386 sgml-base all 1.30 [15.1 kB] Get: 23 http://deb.debian.org/debian bullseye/main i386 libncurses6 i386 6.2+20201114-2+deb11u2 [110 kB] Get: 24 http://deb.debian.org/debian bullseye/main i386 libprocps8 i386 2:3.3.17-5 [64.2 kB] Get: 25 http://deb.debian.org/debian bullseye/main i386 procps i386 2:3.3.17-5 [501 kB] Get: 26 http://deb.debian.org/debian bullseye/main i386 sensible-utils all 0.0.14 [14.8 kB] Get: 27 http://deb.debian.org/debian bullseye/main i386 openssl i386 1.1.1w-0+deb11u1 [869 kB] Get: 28 http://deb.debian.org/debian bullseye/main i386 ca-certificates all 20210119 [158 kB] Get: 29 http://deb.debian.org/debian bullseye/main i386 libmagic-mgc i386 1:5.39-3+deb11u1 [273 kB] Get: 30 http://deb.debian.org/debian bullseye/main i386 libmagic1 i386 1:5.39-3+deb11u1 [135 kB] Get: 31 http://deb.debian.org/debian bullseye/main i386 file i386 1:5.39-3+deb11u1 [69.2 kB] Get: 32 http://deb.debian.org/debian bullseye/main i386 gettext-base i386 0.21-4 [176 kB] Get: 33 http://deb.debian.org/debian bullseye/main i386 libsigsegv2 i386 2.13-1 [35.1 kB] Get: 34 http://deb.debian.org/debian bullseye/main i386 m4 i386 1.4.18-5 [206 kB] Get: 35 http://deb.debian.org/debian bullseye/main i386 autoconf all 2.69-14 [313 kB] Get: 36 http://deb.debian.org/debian bullseye/main i386 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 37 http://deb.debian.org/debian bullseye/main i386 automake all 1:1.16.3-2 [814 kB] Get: 38 http://deb.debian.org/debian bullseye/main i386 autopoint all 0.21-4 [510 kB] Get: 39 http://deb.debian.org/debian bullseye/main i386 cython3 i386 0.29.21-3+b1 [1303 kB] Get: 40 http://deb.debian.org/debian bullseye/main i386 libdebhelper-perl all 13.3.4 [189 kB] Get: 41 http://deb.debian.org/debian bullseye/main i386 libtool all 2.4.6-15 [513 kB] Get: 42 http://deb.debian.org/debian bullseye/main i386 dh-autoreconf all 20 [17.1 kB] Get: 43 http://deb.debian.org/debian bullseye/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 44 http://deb.debian.org/debian bullseye/main i386 libsub-override-perl all 0.09-2 [10.2 kB] Get: 45 http://deb.debian.org/debian bullseye/main i386 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 46 http://deb.debian.org/debian bullseye/main i386 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 47 http://deb.debian.org/debian bullseye/main i386 libelf1 i386 0.183-1 [171 kB] Get: 48 http://deb.debian.org/debian bullseye/main i386 dwz i386 0.13+20210201-1 [179 kB] Get: 49 http://deb.debian.org/debian bullseye/main i386 libicu67 i386 67.1-7 [8775 kB] Get: 50 http://deb.debian.org/debian bullseye/main i386 libxml2 i386 2.9.10+dfsg-6.7+deb11u4 [728 kB] Get: 51 http://deb.debian.org/debian bullseye/main i386 gettext i386 0.21-4 [1322 kB] Get: 52 http://deb.debian.org/debian bullseye/main i386 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 53 http://deb.debian.org/debian bullseye/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 54 http://deb.debian.org/debian bullseye/main i386 debhelper all 13.3.4 [1049 kB] Get: 55 http://deb.debian.org/debian bullseye/main i386 python3-lib2to3 all 3.9.2-1 [77.8 kB] Get: 56 http://deb.debian.org/debian bullseye/main i386 python3-distutils all 3.9.2-1 [143 kB] Get: 57 http://deb.debian.org/debian bullseye/main i386 dh-python all 4.20201102+nmu1 [99.4 kB] Get: 58 http://deb.debian.org/debian bullseye/main i386 xml-core all 0.18+nmu1 [23.8 kB] Get: 59 http://deb.debian.org/debian bullseye/main i386 docutils-common all 0.16+dfsg-4 [129 kB] Get: 60 http://deb.debian.org/debian bullseye/main i386 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [517 kB] Get: 61 http://deb.debian.org/debian bullseye/main i386 fonts-lyx all 2.3.6-1 [205 kB] Get: 62 http://deb.debian.org/debian bullseye/main i386 fonts-mathjax all 2.7.9+dfsg-1 [2210 kB] Get: 63 http://deb.debian.org/debian bullseye/main i386 libaec0 i386 1.0.4-1 [22.6 kB] Get: 64 http://deb.debian.org/debian bullseye/main i386 libblas3 i386 3.9.0-3+deb11u1 [147 kB] Get: 65 http://deb.debian.org/debian bullseye/main i386 libsnappy1v5 i386 1.1.8-1 [19.0 kB] Get: 66 http://deb.debian.org/debian bullseye/main i386 libblosc1 i386 1.20.1+ds1-2 [50.5 kB] Get: 67 http://deb.debian.org/debian bullseye/main i386 libbrotli1 i386 1.0.9-2+b2 [286 kB] Get: 68 http://deb.debian.org/debian bullseye/main i386 libmd0 i386 1.0.3-3 [28.9 kB] Get: 69 http://deb.debian.org/debian bullseye/main i386 libbsd0 i386 0.11.3-1+deb11u1 [111 kB] Get: 70 http://deb.debian.org/debian bullseye/main i386 libdeflate0 i386 1.7-1 [48.4 kB] Get: 71 http://deb.debian.org/debian bullseye/main i386 libexpat1-dev i386 2.2.10-2+deb11u5 [149 kB] Get: 72 http://deb.debian.org/debian bullseye/main i386 libpng16-16 i386 1.6.37-3 [303 kB] Get: 73 http://deb.debian.org/debian bullseye/main i386 libfreetype6 i386 2.10.4+dfsg-1+deb11u1 [430 kB] Get: 74 http://deb.debian.org/debian bullseye/main i386 libgfortran5 i386 10.2.1-6 [643 kB] Get: 75 http://deb.debian.org/debian bullseye/main i386 libsz2 i386 1.0.4-1 [6820 B] Get: 76 http://deb.debian.org/debian bullseye/main i386 libhdf5-103-1 i386 1.10.6+repack-4+deb11u1 [1160 kB] Get: 77 http://deb.debian.org/debian bullseye/main i386 libimagequant0 i386 2.12.2-1.1 [32.4 kB] Get: 78 http://deb.debian.org/debian bullseye/main i386 libjbig0 i386 2.1-3.1+b2 [31.5 kB] Get: 79 http://deb.debian.org/debian bullseye/main i386 libjpeg62-turbo i386 1:2.0.6-4 [160 kB] Get: 80 http://deb.debian.org/debian bullseye/main i386 libjs-jquery all 3.5.1+dfsg+~3.5.5-7 [315 kB] Get: 81 http://deb.debian.org/debian bullseye/main i386 libjs-jquery-ui all 1.12.1+dfsg-8+deb11u1 [232 kB] Get: 82 http://deb.debian.org/debian bullseye/main i386 libjs-mathjax all 2.7.9+dfsg-1 [5667 kB] Get: 83 http://deb.debian.org/debian bullseye/main i386 libjs-underscore all 1.9.1~dfsg-3 [100 kB] Get: 84 http://deb.debian.org/debian bullseye/main i386 libjs-sphinxdoc all 3.4.3-2 [127 kB] Get: 85 http://deb.debian.org/debian bullseye/main i386 liblapack3 i386 3.9.0-3+deb11u1 [1960 kB] Get: 86 http://deb.debian.org/debian bullseye/main i386 liblbfgsb0 i386 3.0+dfsg.3-9 [28.4 kB] Get: 87 http://deb.debian.org/debian bullseye/main i386 liblcms2-2 i386 2.12~rc1-2 [161 kB] Get: 88 http://deb.debian.org/debian bullseye/main i386 liblzo2-2 i386 2.10-2 [59.7 kB] Get: 89 http://deb.debian.org/debian bullseye/main i386 libnorm1 i386 1.5.9+dfsg-2 [238 kB] Get: 90 http://deb.debian.org/debian bullseye/main i386 libpgm-5.3-0 i386 5.3.128~dfsg-2 [168 kB] Get: 91 http://deb.debian.org/debian bullseye/main i386 libpython3.9 i386 3.9.2-1 [1715 kB] Get: 92 http://deb.debian.org/debian bullseye/main i386 libpython3.9-dev i386 3.9.2-1 [3822 kB] Get: 93 http://deb.debian.org/debian bullseye/main i386 libpython3-dev i386 3.9.2-3 [21.7 kB] Get: 94 http://deb.debian.org/debian bullseye/main i386 libpython3-all-dev i386 3.9.2-3 [1068 B] Get: 95 http://deb.debian.org/debian bullseye/main i386 libsodium23 i386 1.0.18-1 [186 kB] Get: 96 http://deb.debian.org/debian bullseye/main i386 libwebp6 i386 0.6.1-2.1+deb11u2 [269 kB] Get: 97 http://deb.debian.org/debian bullseye/main i386 libtiff5 i386 4.2.0-1+deb11u4 [305 kB] Get: 98 http://deb.debian.org/debian bullseye/main i386 libwebpdemux2 i386 0.6.1-2.1+deb11u2 [88.2 kB] Get: 99 http://deb.debian.org/debian bullseye/main i386 libwebpmux3 i386 0.6.1-2.1+deb11u2 [99.0 kB] Get: 100 http://deb.debian.org/debian bullseye/main i386 libxau6 i386 1:1.0.9-1 [20.0 kB] Get: 101 http://deb.debian.org/debian bullseye/main i386 libxdmcp6 i386 1:1.1.2-3 [26.7 kB] Get: 102 http://deb.debian.org/debian bullseye/main i386 libxcb1 i386 1.14-3 [144 kB] Get: 103 http://deb.debian.org/debian bullseye/main i386 libzmq5 i386 4.3.4-1 [300 kB] Get: 104 http://deb.debian.org/debian bullseye/main i386 python-babel-localedata all 2.8.0+dfsg.1-7 [4997 kB] Get: 105 http://deb.debian.org/debian bullseye/main i386 ttf-bitstream-vera all 1.10-8.1 [223 kB] Get: 106 http://deb.debian.org/debian bullseye/main i386 python-matplotlib-data all 3.3.4-1 [4153 kB] Get: 107 http://deb.debian.org/debian bullseye/main i386 python-tables-data all 3.6.1-3 [53.1 kB] Get: 108 http://deb.debian.org/debian bullseye/main i386 python3-alabaster all 0.7.8-1.1 [18.6 kB] Get: 109 http://deb.debian.org/debian bullseye/main i386 python3-all i386 3.9.2-3 [1060 B] Get: 110 http://deb.debian.org/debian bullseye/main i386 zlib1g-dev i386 1:1.2.11.dfsg-2+deb11u2 [194 kB] Get: 111 http://deb.debian.org/debian bullseye/main i386 python3.9-dev i386 3.9.2-1 [515 kB] Get: 112 http://deb.debian.org/debian bullseye/main i386 python3-dev i386 3.9.2-3 [24.8 kB] Get: 113 http://deb.debian.org/debian bullseye/main i386 python3-all-dev i386 3.9.2-3 [1068 B] Get: 114 http://deb.debian.org/debian bullseye/main i386 python3-astor all 0.8.1-1 [23.2 kB] Get: 115 http://deb.debian.org/debian bullseye/main i386 python3-attr all 20.3.0-1 [52.9 kB] Get: 116 http://deb.debian.org/debian bullseye/main i386 python3-pkg-resources all 52.0.0-4 [190 kB] Get: 117 http://deb.debian.org/debian bullseye/main i386 python3-tz all 2021.1-1 [34.8 kB] Get: 118 http://deb.debian.org/debian bullseye/main i386 python3-babel all 2.8.0+dfsg.1-7 [100 kB] Get: 119 http://deb.debian.org/debian bullseye/main i386 python3-backcall all 0.2.0-1 [10.7 kB] Get: 120 http://deb.debian.org/debian bullseye/main i386 python3-pyparsing all 2.4.7-1 [109 kB] Get: 121 http://deb.debian.org/debian bullseye/main i386 python3-packaging all 20.9-2 [33.5 kB] Get: 122 http://deb.debian.org/debian bullseye/main i386 python3-six all 1.16.0-2 [17.5 kB] Get: 123 http://deb.debian.org/debian bullseye/main i386 python3-webencodings all 0.5.1-2 [11.0 kB] Get: 124 http://deb.debian.org/debian bullseye/main i386 python3-html5lib all 1.1-3 [93.0 kB] Get: 125 http://deb.debian.org/debian bullseye/main i386 python3-bleach all 3.2.1-2.1 [36.5 kB] Get: 126 http://deb.debian.org/debian bullseye/main i386 python3-certifi all 2020.6.20-1 [151 kB] Get: 127 http://deb.debian.org/debian bullseye/main i386 python3-chardet all 4.0.0-1 [99.0 kB] Get: 128 http://deb.debian.org/debian bullseye/main i386 python3-cycler all 0.10.0-3 [8084 B] Get: 129 http://deb.debian.org/debian bullseye/main i386 python3-dateutil all 2.8.1-6 [79.2 kB] Get: 130 http://deb.debian.org/debian bullseye/main i386 python3-decorator all 4.4.2-2 [15.8 kB] Get: 131 http://deb.debian.org/debian bullseye/main i386 python3-defusedxml all 0.6.0-2 [38.2 kB] Get: 132 http://deb.debian.org/debian bullseye/main i386 python3-roman all 2.0.0-5 [9064 B] Get: 133 http://deb.debian.org/debian bullseye/main i386 python3-docutils all 0.16+dfsg-4 [384 kB] Get: 134 http://deb.debian.org/debian bullseye/main i386 python3-entrypoints all 0.3-5 [5848 B] Get: 135 http://deb.debian.org/debian bullseye/main i386 python3-idna all 2.10-1 [37.4 kB] Get: 136 http://deb.debian.org/debian bullseye/main i386 python3-imagesize all 1.2.0-2 [5824 B] Get: 137 http://deb.debian.org/debian bullseye/main i386 python3-more-itertools all 4.2.0-3 [42.7 kB] Get: 138 http://deb.debian.org/debian bullseye/main i386 python3-zipp all 1.0.0-3 [6060 B] Get: 139 http://deb.debian.org/debian bullseye/main i386 python3-importlib-metadata all 1.6.0-2 [10.3 kB] Get: 140 http://deb.debian.org/debian bullseye/main i386 python3-parso all 0.8.1-1 [65.9 kB] Get: 141 http://deb.debian.org/debian bullseye/main i386 python3-jedi all 0.18.0-1 [620 kB] Get: 142 http://deb.debian.org/debian bullseye/main i386 python3-ptyprocess all 0.7.0-1 [13.6 kB] Get: 143 http://deb.debian.org/debian bullseye/main i386 python3-pexpect all 4.8.0-2 [54.9 kB] Get: 144 http://deb.debian.org/debian bullseye/main i386 python3-pickleshare all 0.7.5-3 [7604 B] Get: 145 http://deb.debian.org/debian bullseye/main i386 python3-wcwidth all 0.1.9+dfsg1-2 [18.2 kB] Get: 146 http://deb.debian.org/debian bullseye/main i386 python3-prompt-toolkit all 3.0.14-1 [258 kB] Get: 147 http://deb.debian.org/debian bullseye/main i386 python3-pygments all 2.7.1+dfsg-2.1 [657 kB] Get: 148 http://deb.debian.org/debian bullseye/main i386 python3-ipython-genutils all 0.2.0-4 [21.4 kB] Get: 149 http://deb.debian.org/debian bullseye/main i386 python3-traitlets all 5.0.5-1 [84.4 kB] Get: 150 http://deb.debian.org/debian bullseye/main i386 python3-ipython all 7.20.0-1+deb11u1 [517 kB] Get: 151 http://deb.debian.org/debian bullseye/main i386 python3-jupyter-core all 4.7.1-1+deb11u1 [44.2 kB] Get: 152 http://deb.debian.org/debian bullseye/main i386 python3-tornado i386 6.1.0-1+b1 [338 kB] Get: 153 http://deb.debian.org/debian bullseye/main i386 python3-zmq i386 20.0.0-1+b1 [263 kB] Get: 154 http://deb.debian.org/debian bullseye/main i386 python3-jupyter-client all 6.1.11-2 [76.6 kB] Get: 155 http://deb.debian.org/debian bullseye/main i386 python3-ipykernel all 5.4.3-1 [84.9 kB] Get: 156 http://deb.debian.org/debian bullseye/main i386 python3-markupsafe i386 1.1.1-1+b3 [15.3 kB] Get: 157 http://deb.debian.org/debian bullseye/main i386 python3-jinja2 all 2.11.3-1 [114 kB] Get: 158 http://deb.debian.org/debian bullseye/main i386 python3-joblib all 0.17.0-4+deb11u1 [214 kB] Get: 159 http://deb.debian.org/debian bullseye/main i386 python3-setuptools all 52.0.0-4 [366 kB] Get: 160 http://deb.debian.org/debian bullseye/main i386 python3-pyrsistent i386 0.15.5-1+b3 [59.3 kB] Get: 161 http://deb.debian.org/debian bullseye/main i386 python3-jsonschema all 3.2.0-3 [46.3 kB] Get: 162 http://deb.debian.org/debian bullseye/main i386 python3-kiwisolver i386 1.3.1-1+b1 [58.5 kB] Get: 163 http://deb.debian.org/debian bullseye/main i386 python3-numpy i386 1:1.19.5-1 [3600 kB] Get: 164 http://deb.debian.org/debian bullseye/main i386 python3-pil i386 8.1.2+dfsg-0.3+deb11u1 [445 kB] Get: 165 http://deb.debian.org/debian bullseye/main i386 python3-matplotlib i386 3.3.4-1 [4165 kB] Get: 166 http://deb.debian.org/debian bullseye/main i386 python3-mistune all 0.8.4-4 [16.4 kB] Get: 167 http://deb.debian.org/debian bullseye/main i386 sphinx-rtd-theme-common all 0.5.1+dfsg-1 [995 kB] Get: 168 http://deb.debian.org/debian bullseye/main i386 sphinx-common all 3.4.3-2 [578 kB] Get: 169 http://deb.debian.org/debian bullseye/main i386 python3-urllib3 all 1.26.5-1~exp1 [114 kB] Get: 170 http://deb.debian.org/debian bullseye/main i386 python3-requests all 2.25.1+dfsg-2 [69.3 kB] Get: 171 http://deb.debian.org/debian bullseye/main i386 python3-snowballstemmer all 2.1.0-1 [58.7 kB] Get: 172 http://deb.debian.org/debian bullseye/main i386 python3-sphinx all 3.4.3-2 [545 kB] Get: 173 http://deb.debian.org/debian bullseye/main i386 python3-sphinx-rtd-theme all 0.5.1+dfsg-1 [20.9 kB] Get: 174 http://deb.debian.org/debian bullseye/main i386 python3-msmb-theme all 1.2.0-2 [33.5 kB] Get: 175 http://deb.debian.org/debian bullseye/main i386 python3-nbformat all 5.1.2-1 [51.6 kB] Get: 176 http://deb.debian.org/debian bullseye/main i386 python3-pandocfilters all 1.4.3-1 [20.0 kB] Get: 177 http://deb.debian.org/debian bullseye/main i386 python3-testpath all 0.4.4+dfsg-1 [8996 B] Get: 178 http://deb.debian.org/debian bullseye/main i386 python3-nbconvert all 5.6.1-3 [356 kB] Get: 179 http://deb.debian.org/debian bullseye/main i386 python3-networkx all 2.5+ds-2 [900 kB] Get: 180 http://deb.debian.org/debian bullseye/main i386 python3-numexpr i386 2.7.2-2 [128 kB] Get: 181 http://deb.debian.org/debian bullseye/main i386 python3-numpydoc all 1.1.0-3 [40.0 kB] Get: 182 http://deb.debian.org/debian bullseye/main i386 python3-pandas-lib i386 1.1.5+dfsg-2 [3182 kB] Get: 183 http://deb.debian.org/debian bullseye/main i386 python3-pandas all 1.1.5+dfsg-2 [2096 kB] Get: 184 http://deb.debian.org/debian bullseye/main i386 python3-scipy i386 1.6.0-2 [11.9 MB] Get: 185 http://deb.debian.org/debian bullseye/main i386 python3-sklearn-lib i386 0.23.2-5 [1789 kB] Get: 186 http://deb.debian.org/debian bullseye/main i386 python3-threadpoolctl all 2.1.0-1 [15.3 kB] Get: 187 http://deb.debian.org/debian bullseye/main i386 python3-sklearn all 0.23.2-5 [1818 kB] Get: 188 http://deb.debian.org/debian bullseye/main i386 python3-tables-lib i386 3.6.1-3 [409 kB] Get: 189 http://deb.debian.org/debian bullseye/main i386 python3-tables all 3.6.1-3 [342 kB] Fetched 103 MB in 2s (58.9 MB/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 ... 17763 files and directories currently installed.) Preparing to unpack .../0-bsdextrautils_2.36.1-8+deb11u1_i386.deb ... Unpacking bsdextrautils (2.36.1-8+deb11u1) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../1-libuchardet0_0.0.7-1_i386.deb ... Unpacking libuchardet0:i386 (0.0.7-1) ... Selecting previously unselected package groff-base. 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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:i386 (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:i386 (5.3.128~dfsg-2) ... Setting up fonts-lyx (2.3.6-1) ... Setting up libdebhelper-perl (13.3.4) ... Setting up libbrotli1:i386 (1.0.9-2+b2) ... Setting up libnorm1:i386 (1.5.9+dfsg-2) ... Setting up libmagic1:i386 (1:5.39-3+deb11u1) ... Setting up libdeflate0:i386 (1.7-1) ... Setting up gettext-base (0.21-4) ... Setting up liblzo2-2:i386 (2.10-2) ... Setting up file (1:5.39-3+deb11u1) ... Setting up libjbig0:i386 (2.1-3.1+b2) ... Setting up libaec0:i386 (1.0.4-1) ... Setting up python-babel-localedata (2.8.0+dfsg.1-7) ... Setting up libsnappy1v5:i386 (1.1.8-1) ... Setting up tzdata (2021a-1+deb11u10) ... Current default time zone: 'Etc/UTC' Local time is now: Sat Feb 8 05:04:00 UTC 2025. Universal Time is now: Sat Feb 8 05:04:00 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20180224.1+nmu1) ... Setting up libblas3:i386 (3.9.0-3+deb11u1) ... update-alternatives: using /usr/lib/i386-linux-gnu/blas/libblas.so.3 to provide /usr/lib/i386-linux-gnu/libblas.so.3 (libblas.so.3-i386-linux-gnu) in auto mode Setting up libexpat1-dev:i386 (2.2.10-2+deb11u5) ... Setting up libjpeg62-turbo:i386 (1:2.0.6-4) ... Setting up libncurses6:i386 (6.2+20201114-2+deb11u2) ... Setting up libsigsegv2:i386 (2.13-1) ... Setting up libimagequant0:i386 (2.12.2-1.1) ... Setting up libpng16-16:i386 (1.6.37-3) ... Setting up autopoint (0.21-4) ... Setting up libwebp6:i386 (0.6.1-2.1+deb11u2) ... Setting up libgfortran5:i386 (10.2.1-6) ... Setting up zlib1g-dev:i386 (1:1.2.11.dfsg-2+deb11u2) ... Setting up libmd0:i386 (1.0.3-3) ... Setting up sensible-utils (0.0.14) ... 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Setting up libxdmcp6:i386 (1:1.1.2-3) ... Setting up liblapack3:i386 (3.9.0-3+deb11u1) ... update-alternatives: using /usr/lib/i386-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/i386-linux-gnu/liblapack.so.3 (liblapack.so.3-i386-linux-gnu) in auto mode Setting up libxcb1:i386 (1.14-3) ... Setting up gettext (0.21-4) ... Setting up libzmq5:i386 (4.3.4-1) ... Setting up mime-support (3.66) ... Setting up libtool (2.4.6-15) ... Setting up libwebpdemux2:i386 (0.6.1-2.1+deb11u2) ... Setting up libreadline8:i386 (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:i386 (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:i386 (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:i386 (3.9.2-1) ... Setting up libpython3-stdlib:i386 (3.9.2-3) ... Setting up liblbfgsb0:i386 (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:i386 (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:i386 (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:i386 (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:i386 (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:i386 (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:i386 (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:i386 (1.1.5+dfsg-2) ... Setting up python3-sklearn-lib:i386 (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: Running cd /build/reproducible-path/mdtraj-1.9.5/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../mdtraj_1.9.5-1_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 i386 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/i686-linux-gnu-gcc COLLECT_LTO_WRAPPER=/usr/lib/gcc/i686-linux-gnu/10/lto-wrapper Target: i686-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=i686-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-targets=all --enable-multiarch --disable-werror --with-arch-32=i686 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-checking=release --build=i686-linux-gnu --host=i686-linux-gnu --target=i686-linux-gnu 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-i386' 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/i686-linux-gnu-gcc COLLECT_LTO_WRAPPER=/usr/lib/gcc/i686-linux-gnu/10/lto-wrapper Target: i686-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=i686-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-targets=all --enable-multiarch --disable-werror --with-arch-32=i686 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-checking=release --build=i686-linux-gnu --host=i686-linux-gnu --target=i686-linux-gnu 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/i686-linux-gnu-gcc COLLECT_LTO_WRAPPER=/usr/lib/gcc/i686-linux-gnu/10/lto-wrapper Target: i686-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=i686-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-targets=all --enable-multiarch --disable-werror --with-arch-32=i686 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-checking=release --build=i686-linux-gnu --host=i686-linux-gnu --target=i686-linux-gnu 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/io.py -> /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/__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/reporters copying mdtraj/reporters/basereporter.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/netcdfreporter.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 copying mdtraj/reporters/xtcreporter.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/core copying mdtraj/core/trajectory.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 copying mdtraj/core/residue_names.py -> /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/topology.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/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 copying mdtraj/testing/testing.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/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 copying mdtraj/nmr/shift_wrappers.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/utils copying mdtraj/utils/zipped.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/singleton.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/__init__.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/delay_import.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/formats copying mdtraj/formats/lh5.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/amberrst.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/registry.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/mdcrd.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/__init__.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/hoomdxml.py -> /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/arc.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/openmmxml.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/hdf5.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/geometry copying mdtraj/geometry/shape.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/contact.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/dihedral.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/angle.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/__init__.py -> /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/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/distance.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/sasa.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/scripts copying mdtraj/scripts/__init__.py -> /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 creating /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/standard_dimensions.py -> /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.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/__init__.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/baseunit.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/quantity.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/basedimension.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 creating /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/pdbstructure.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-i386-3.9 creating build/temp.linux-i386-3.9/mdtraj creating build/temp.linux-i386-3.9/mdtraj/formats creating build/temp.linux-i386-3.9/mdtraj/formats/xtc creating build/temp.linux-i386-3.9/mdtraj/formats/xtc/src i686-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-hfHQKB/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-i386-3.9/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-hfHQKB/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-i386-3.9/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; | ^~~~~~ i686-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-hfHQKB/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-i386-3.9/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 { | ^~ i686-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-hfHQKB/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-i386-3.9/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; | ^ i686-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-i386-3.9/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-i386-3.9/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-i386-3.9/mdtraj/formats/xtc/src/xdrfile_xtc.o build/temp.linux-i386-3.9/mdtraj/formats/xtc/xtc.o -o /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/xtc.cpython-39-i386-linux-gnu.so building 'mdtraj.formats.trr' extension i686-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-hfHQKB/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-i386-3.9/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-hfHQKB/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-i386-3.9/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; | ^~~~~~ i686-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-hfHQKB/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-i386-3.9/mdtraj/formats/xtc/src/xdrfile_trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-hfHQKB/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-i386-3.9/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:1775:95: 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:8249:59: warning: '__pyx_pybuffernd_forces.diminfo[0].shape' may be used uninitialized in this function [-Wmaybe-uninitialized] 8249 | __pyx_t_29 += __pyx_pybuffernd_forces.diminfo[0].shape; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ 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:1775:95: 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:8192:56: warning: '__pyx_pybuffernd_vel.diminfo[0].shape' may be used uninitialized in this function [-Wmaybe-uninitialized] 8192 | __pyx_t_29 += __pyx_pybuffernd_vel.diminfo[0].shape; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ 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; | ^ i686-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-i386-3.9/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-i386-3.9/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-i386-3.9/mdtraj/formats/xtc/src/xdrfile_trr.o build/temp.linux-i386-3.9/mdtraj/formats/xtc/trr.o -o /build/reproducible-path/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/trr.cpython-39-i386-linux-gnu.so building 'mdtraj.formats.tng' extension creating build/temp.linux-i386-3.9/mdtraj/formats/tng creating build/temp.linux-i386-3.9/mdtraj/formats/tng/src creating build/temp.linux-i386-3.9/mdtraj/formats/tng/src/compression creating build/temp.linux-i386-3.9/mdtraj/formats/tng/src/lib i686-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-hfHQKB/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-i386-3.9/mdtraj/formats/tng/src/compression/bwlzh.o i686-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-hfHQKB/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-i386-3.9/mdtraj/formats/tng/src/compression/bwt.o i686-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-hfHQKB/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-i386-3.9/mdtraj/formats/tng/src/compression/coder.o i686-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-hfHQKB/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-i386-3.9/mdtraj/formats/tng/src/compression/dict.o i686-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-hfHQKB/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-i386-3.9/mdtraj/formats/tng/src/compression/fixpoint.o i686-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-hfHQKB/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-i386-3.9/mdtraj/formats/tng/src/compression/huffman.o i686-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-hfHQKB/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-i386-3.9/mdtraj/formats/tng/src/compression/huffmem.o i686-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-hfHQKB/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-i386-3.9/mdtraj/formats/tng/src/compression/lz77.o i686-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-hfHQKB/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-i386-3.9/mdtraj/formats/tng/src/compression/merge_sort.o i686-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-hfHQKB/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-i386-3.9/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) | ^~ i686-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-hfHQKB/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-i386-3.9/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]) | ^~ i686-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-hfHQKB/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-i386-3.9/mdtraj/formats/tng/src/compression/tng_compress.o i686-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-hfHQKB/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-i386-3.9/mdtraj/formats/tng/src/compression/vals16.o i686-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-hfHQKB/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-i386-3.9/mdtraj/formats/tng/src/compression/warnmalloc.o i686-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-hfHQKB/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-i386-3.9/mdtraj/formats/tng/src/compression/widemuldiv.o i686-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-hfHQKB/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-i386-3.9/mdtraj/formats/tng/src/compression/xtc2.o i686-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-hfHQKB/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-i386-3.9/mdtraj/formats/tng/src/compression/xtc3.o i686-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-hfHQKB/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-i386-3.9/mdtraj/formats/tng/src/lib/md5.o i686-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-hfHQKB/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-i386-3.9/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 long int *)'} from incompatible pointer type 'tng_function_status (*)(struct tng_trajectory * const, uint64_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, long 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 long int *)'} from incompatible pointer type 'tng_function_status (*)(struct tng_trajectory * const, uint64_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, long 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 long int *)'} from incompatible pointer type 'tng_function_status (*)(struct tng_trajectory * const, uint64_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, long 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 long int *)'} from incompatible pointer type 'tng_function_status (*)(struct tng_trajectory * const, uint64_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, long 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/i386-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; | ^~~~~~~~~~~ i686-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-hfHQKB/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-i386-3.9/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); | ^~ i686-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-i386-3.9/mdtraj/formats/tng/src/compression/bwlzh.o build/temp.linux-i386-3.9/mdtraj/formats/tng/src/compression/bwt.o build/temp.linux-i386-3.9/mdtraj/formats/tng/src/compression/coder.o build/temp.linux-i386-3.9/mdtraj/formats/tng/src/compression/dict.o build/temp.linux-i386-3.9/mdtraj/formats/tng/src/compression/fixpoint.o build/temp.linux-i386-3.9/mdtraj/formats/tng/src/compression/huffman.o build/temp.linux-i386-3.9/mdtraj/formats/tng/src/compression/huffmem.o build/temp.linux-i386-3.9/mdtraj/formats/tng/src/compression/lz77.o build/temp.linux-i386-3.9/mdtraj/formats/tng/src/compression/merge_sort.o build/temp.linux-i386-3.9/mdtraj/formats/tng/src/compression/mtf.o build/temp.linux-i386-3.9/mdtraj/formats/tng/src/compression/rle.o build/temp.linux-i386-3.9/mdtraj/formats/tng/src/compression/tng_compress.o build/temp.linux-i386-3.9/mdtraj/formats/tng/src/compression/vals16.o build/temp.linux-i386-3.9/mdtraj/formats/tng/src/compression/warnmalloc.o build/temp.linux-i386-3.9/mdtraj/formats/tng/src/compression/widemuldiv.o build/temp.linux-i386-3.9/mdtraj/formats/tng/src/compression/xtc2.o build/temp.linux-i386-3.9/mdtraj/formats/tng/src/compression/xtc3.o build/temp.linux-i386-3.9/mdtraj/formats/tng/src/lib/md5.o build/temp.linux-i386-3.9/mdtraj/formats/tng/src/lib/tng_io.o build/temp.linux-i386-3.9/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-i386-linux-gnu.so building 'mdtraj.formats.dcd' extension creating build/temp.linux-i386-3.9/mdtraj/formats/dcd creating build/temp.linux-i386-3.9/mdtraj/formats/dcd/src i686-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-hfHQKB/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-i386-3.9/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; | ^~~~~~~~~ i686-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-hfHQKB/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-i386-3.9/mdtraj/formats/dcd/src/dcdplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-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-i386-3.9/mdtraj/formats/dcd/dcd.o build/temp.linux-i386-3.9/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-i386-linux-gnu.so building 'mdtraj.formats.binpos' extension creating build/temp.linux-i386-3.9/mdtraj/formats/binpos creating build/temp.linux-i386-3.9/mdtraj/formats/binpos/src i686-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-hfHQKB/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-i386-3.9/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; | ^~~~~~~~~ i686-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-hfHQKB/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-i386-3.9/mdtraj/formats/binpos/src/binposplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-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-i386-3.9/mdtraj/formats/binpos/binpos.o build/temp.linux-i386-3.9/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-i386-linux-gnu.so building 'mdtraj.formats.dtr' extension creating build/temp.linux-i386-3.9/mdtraj/formats/dtr creating build/temp.linux-i386-3.9/mdtraj/formats/dtr/src i686-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-hfHQKB/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-i386-3.9/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 " \ | ^~~~~~~ i686-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-hfHQKB/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-i386-3.9/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:486:64: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 486 | fprintf(stderr, "non-constant framesize at frame %ld\n", i); | ~~^ ~ | | | | | size_t {aka unsigned int} | long int | %d 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 long unsigned int'} [-Wformat=] 487 | printf("size %d framesize %d\n\n", | ~^ | | | int | %lld 488 | keys[i].size(), m_framesize); | ~~~~~~~~~~~~~~ | | | uint64_t {aka long 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 long unsigned int'} [-Wformat=] 487 | printf("size %d framesize %d\n\n", | ~^ | | | int | %lld 488 | keys[i].size(), m_framesize); | ~~~~~~~~~~~ | | | uint64_t {aka long long unsigned int} mdtraj/formats/dtr/src/dtrplugin.cxx:494:60: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 494 | "non-constant time interval at frame %ld\n", i); | ~~^ ~ | | | | | size_t {aka unsigned int} | long int | %d mdtraj/formats/dtr/src/dtrplugin.cxx:499:60: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 499 | fprintf(stderr, "unexpected offset for frame %ld\n", i); | ~~^ ~ | | | | | size_t {aka unsigned int} | long int | %d mdtraj/formats/dtr/src/dtrplugin.cxx: In function 'int handle_wrapped_v2({anonymous}::BlobMap&, uint32_t, bool, molfile_timestep_t*)': mdtraj/formats/dtr/src/dtrplugin.cxx:1301:69: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'uint64_t' {aka 'long long unsigned int'} [-Wformat=] 1301 | fprintf(stderr, "ERROR, Expected %d elements in POSITION; got %ld\n", | ~~^ | | | long int | %lld 1302 | 3*natoms, pos.count); | ~~~~~~~~~ | | | uint64_t {aka long long unsigned int} mdtraj/formats/dtr/src/dtrplugin.cxx:1310:71: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'uint64_t' {aka 'long long unsigned int'} [-Wformat=] 1310 | fprintf(stderr, "ERROR, Expected %d elements in VELOCITY; got %ld\n", | ~~^ | | | long int | %lld 1311 | 3*natoms, vel.count); | ~~~~~~~~~ | | | uint64_t {aka long long unsigned int} mdtraj/formats/dtr/src/dtrplugin.cxx: In function 'int handle_wrapped_v1({anonymous}::BlobMap&, uint32_t, bool, molfile_timestep_t*)': mdtraj/formats/dtr/src/dtrplugin.cxx:1572:45: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'uint64_t' {aka 'long long unsigned int'} [-Wformat=] 1572 | fprintf(stderr, "VELOCITY field has %ld values; expected %d\n", | ~~^ | | | long int | %lld 1573 | velblob.count, 3*natoms); | ~~~~~~~~~~~~~ | | | uint64_t {aka long 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/i386-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/i386-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/i386-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/i386-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 ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ i686-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-i386-3.9/mdtraj/formats/dtr/dtr.o build/temp.linux-i386-3.9/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-i386-linux-gnu.so building 'mdtraj._rmsd' extension creating build/temp.linux-i386-3.9/mdtraj/rmsd creating build/temp.linux-i386-3.9/mdtraj/rmsd/src i686-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-hfHQKB/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-i386-3.9/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); | ^~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-hfHQKB/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-i386-3.9/mdtraj/rmsd/src/center.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-hfHQKB/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-i386-3.9/mdtraj/rmsd/src/rotation.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-hfHQKB/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-i386-3.9/mdtraj/rmsd/src/theobald_rmsd.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-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-i386-3.9/mdtraj/rmsd/_rmsd.o build/temp.linux-i386-3.9/mdtraj/rmsd/src/center.o build/temp.linux-i386-3.9/mdtraj/rmsd/src/rotation.o build/temp.linux-i386-3.9/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-i386-linux-gnu.so building 'mdtraj._lprmsd' extension i686-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-hfHQKB/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-i386-3.9/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; | ^~ i686-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-hfHQKB/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-i386-3.9/mdtraj/rmsd/src/Munkres.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-hfHQKB/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-i386-3.9/mdtraj/rmsd/src/center.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-hfHQKB/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-i386-3.9/mdtraj/rmsd/src/euclidean_permutation.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-hfHQKB/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-i386-3.9/mdtraj/rmsd/src/fancy_index.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-hfHQKB/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-i386-3.9/mdtraj/rmsd/src/rotation.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-hfHQKB/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-i386-3.9/mdtraj/rmsd/src/theobald_rmsd.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-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-i386-3.9/mdtraj/rmsd/_lprmsd.o build/temp.linux-i386-3.9/mdtraj/rmsd/src/Munkres.o build/temp.linux-i386-3.9/mdtraj/rmsd/src/center.o build/temp.linux-i386-3.9/mdtraj/rmsd/src/euclidean_permutation.o build/temp.linux-i386-3.9/mdtraj/rmsd/src/fancy_index.o build/temp.linux-i386-3.9/mdtraj/rmsd/src/rotation.o build/temp.linux-i386-3.9/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-i386-linux-gnu.so building 'mdtraj.core.lib.libtheobald' extension i686-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-hfHQKB/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-i386-3.9/mdtraj/rmsd/src/theobald_rmsd.o -msse2 -mssse3 -O3 -funroll-loops i686-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-hfHQKB/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-i386-3.9/mdtraj/rmsd/src/center.o -msse2 -mssse3 -O3 -funroll-loops i686-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-i386-3.9/mdtraj/rmsd/src/theobald_rmsd.o build/temp.linux-i386-3.9/mdtraj/rmsd/src/center.o building 'mdtraj.geometry._geometry' extension creating build/temp.linux-i386-3.9/mdtraj/geometry creating build/temp.linux-i386-3.9/mdtraj/geometry/src i686-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-hfHQKB/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-i386-3.9/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] i686-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-hfHQKB/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-i386-3.9/mdtraj/geometry/src/dssp.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-hfHQKB/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-i386-3.9/mdtraj/geometry/src/geometry.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-hfHQKB/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-i386-3.9/mdtraj/geometry/src/sasa.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-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-i386-3.9/mdtraj/geometry/src/_geometry.o build/temp.linux-i386-3.9/mdtraj/geometry/src/dssp.o build/temp.linux-i386-3.9/mdtraj/geometry/src/geometry.o build/temp.linux-i386-3.9/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-i386-linux-gnu.so building 'mdtraj.geometry.drid' extension i686-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-hfHQKB/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-i386-3.9/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); | ^~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-hfHQKB/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-i386-3.9/mdtraj/geometry/src/dridkernels.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-hfHQKB/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-i386-3.9/mdtraj/geometry/src/moments.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-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-i386-3.9/mdtraj/geometry/drid.o build/temp.linux-i386-3.9/mdtraj/geometry/src/dridkernels.o build/temp.linux-i386-3.9/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-i386-linux-gnu.so building 'mdtraj.geometry.neighbors' extension i686-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-hfHQKB/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-i386-3.9/mdtraj/geometry/neighbors.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-hfHQKB/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-i386-3.9/mdtraj/geometry/src/neighbors.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-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-i386-3.9/mdtraj/geometry/neighbors.o build/temp.linux-i386-3.9/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-i386-linux-gnu.so building 'mdtraj.geometry.neighborlist' extension i686-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-hfHQKB/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-i386-3.9/mdtraj/geometry/neighborlist.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-hfHQKB/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-i386-3.9/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 || | ~~~~~~~~~~~~~~~~~~~~~~~^ i686-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-i386-3.9/mdtraj/geometry/neighborlist.o build/temp.linux-i386-3.9/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-i386-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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[ 47%] api/generated/mdtraj.load_arc reading sources... [ 48%] api/generated/mdtraj.load_binpos reading sources... [ 48%] api/generated/mdtraj.load_dcd reading sources... [ 49%] api/generated/mdtraj.load_dtr reading sources... [ 50%] api/generated/mdtraj.load_frame reading sources... [ 51%] api/generated/mdtraj.load_hdf5 reading sources... [ 51%] api/generated/mdtraj.load_hoomdxml reading sources... [ 52%] api/generated/mdtraj.load_lammpstrj reading sources... [ 53%] api/generated/mdtraj.load_lh5 reading sources... [ 54%] api/generated/mdtraj.load_netcdf reading sources... [ 55%] api/generated/mdtraj.load_pdb reading sources... [ 55%] api/generated/mdtraj.load_prmtop reading sources... [ 56%] api/generated/mdtraj.load_trr reading sources... [ 57%] api/generated/mdtraj.load_xml reading sources... [ 58%] api/generated/mdtraj.load_xtc reading sources... [ 59%] api/generated/mdtraj.load_xyz reading sources... [ 59%] api/generated/mdtraj.lprmsd reading sources... [ 60%] api/generated/mdtraj.open reading sources... [ 61%] api/generated/mdtraj.principal_moments reading sources... [ 62%] api/generated/mdtraj.reindex_dataframe_by_atoms reading sources... [ 62%] api/generated/mdtraj.relative_shape_antisotropy reading sources... [ 63%] api/generated/mdtraj.reporters.DCDReporter reading sources... [ 64%] api/generated/mdtraj.reporters.HDF5Reporter reading sources... [ 65%] api/generated/mdtraj.reporters.NetCDFReporter reading sources... [ 66%] api/generated/mdtraj.rmsd reading sources... [ 66%] api/generated/mdtraj.rmsf reading sources... [ 67%] api/generated/mdtraj.shrake_rupley reading sources... [ 68%] api/generated/mdtraj.static_dielectric reading sources... [ 69%] api/generated/mdtraj.thermal_expansion_alpha_P reading sources... [ 70%] api/generated/mdtraj.utils.box_vectors_to_lengths_and_angles reading sources... [ 70%] api/generated/mdtraj.utils.check_random_state reading sources... 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[ 82%] examples/atom-selection /usr/lib/python3/dist-packages/IPython/paths.py:66: UserWarning: IPython parent '/nonexistent/first-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/first-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/first-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/first-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/first-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/first-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/first-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/first-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... [ 86%] examples/introduction reading sources... [ 87%] examples/iterload /usr/lib/python3/dist-packages/IPython/paths.py:66: UserWarning: IPython parent '/nonexistent/first-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/first-build' is not a writable location, using a temp directory. warn("IPython parent '{0}' is not a writable location," reading sources... [ 88%] examples/native-contact /usr/lib/python3/dist-packages/IPython/paths.py:66: UserWarning: IPython parent '/nonexistent/first-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/first-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/first-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/first-build' is not a writable location, using a temp directory. warn("IPython parent '{0}' is not a writable location," reading sources... [ 89%] examples/openmm /usr/lib/python3/dist-packages/IPython/paths.py:66: UserWarning: IPython parent '/nonexistent/first-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/first-build' is not a writable location, using a temp directory. warn("IPython parent '{0}' is not a writable location," reading sources... [ 90%] examples/pca /usr/lib/python3/dist-packages/IPython/paths.py:66: UserWarning: IPython parent '/nonexistent/first-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/first-build' is not a writable location, using a temp directory. warn("IPython parent '{0}' is not a writable location," reading sources... [ 91%] examples/ramachandran-plot /usr/lib/python3/dist-packages/IPython/paths.py:66: UserWarning: IPython parent '/nonexistent/first-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/first-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/first-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/first-build' is not a writable location, using a temp directory. warn("IPython parent '{0}' is not a writable location," reading sources... [ 92%] examples/solvent-accessible-surface-area /usr/lib/python3/dist-packages/IPython/paths.py:66: UserWarning: IPython parent '/nonexistent/first-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/first-build' is not a writable location, using a temp directory. warn("IPython parent '{0}' is not a writable location," reading sources... [ 93%] examples/two-pass-clustering /usr/lib/python3/dist-packages/IPython/paths.py:66: UserWarning: IPython parent '/nonexistent/first-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/first-build' is not a writable location, using a temp directory. warn("IPython parent '{0}' is not a writable location," reading sources... [ 94%] faq reading sources... [ 95%] hdf5_format reading sources... [ 96%] index reading sources... [ 96%] installation reading sources... [ 97%] load_functions reading sources... [ 98%] mdconvert reading sources... [ 99%] new_to_python reading sources... [100%] whatsnew /build/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... [ 3%] api/generated/mdtraj.Trajectory.superpose writing output... [ 3%] api/generated/mdtraj.acylindricity writing output... [ 4%] api/generated/mdtraj.asphericity writing output... [ 5%] api/generated/mdtraj.baker_hubbard writing output... [ 6%] api/generated/mdtraj.chemical_shifts_ppm writing output... [ 7%] api/generated/mdtraj.chemical_shifts_shiftx2 writing output... [ 7%] api/generated/mdtraj.chemical_shifts_spartaplus writing output... [ 8%] api/generated/mdtraj.compute_J3_HN_C writing output... [ 9%] api/generated/mdtraj.compute_J3_HN_CB writing output... [ 10%] api/generated/mdtraj.compute_J3_HN_HA writing output... [ 11%] api/generated/mdtraj.compute_angles writing output... [ 11%] api/generated/mdtraj.compute_center_of_mass writing output... [ 12%] api/generated/mdtraj.compute_chi1 writing output... [ 13%] api/generated/mdtraj.compute_chi2 writing output... [ 14%] api/generated/mdtraj.compute_chi3 writing output... [ 14%] api/generated/mdtraj.compute_chi4 writing output... [ 15%] api/generated/mdtraj.compute_contacts writing output... [ 16%] api/generated/mdtraj.compute_dihedrals writing output... [ 17%] api/generated/mdtraj.compute_directors writing output... [ 18%] api/generated/mdtraj.compute_displacements writing output... [ 18%] api/generated/mdtraj.compute_distances writing output... [ 19%] api/generated/mdtraj.compute_drid writing output... [ 20%] api/generated/mdtraj.compute_dssp writing output... [ 21%] api/generated/mdtraj.compute_gyration_tensor writing output... [ 22%] api/generated/mdtraj.compute_inertia_tensor writing output... [ 22%] api/generated/mdtraj.compute_neighbors writing output... [ 23%] api/generated/mdtraj.compute_nematic_order writing output... [ 24%] api/generated/mdtraj.compute_omega writing output... [ 25%] api/generated/mdtraj.compute_phi writing output... [ 25%] api/generated/mdtraj.compute_psi writing output... [ 26%] api/generated/mdtraj.compute_rdf writing output... [ 27%] api/generated/mdtraj.compute_rg writing output... [ 28%] api/generated/mdtraj.density writing output... [ 29%] api/generated/mdtraj.dipole_moments writing output... [ 29%] api/generated/mdtraj.formats.AmberNetCDFRestartFile writing output... [ 30%] api/generated/mdtraj.formats.AmberRestartFile writing output... [ 31%] api/generated/mdtraj.formats.ArcTrajectoryFile writing output... [ 32%] api/generated/mdtraj.formats.BINPOSTrajectoryFile writing output... [ 33%] api/generated/mdtraj.formats.DCDTrajectoryFile writing output... [ 33%] api/generated/mdtraj.formats.DTRTrajectoryFile writing output... [ 34%] api/generated/mdtraj.formats.GroTrajectoryFile writing output... [ 35%] api/generated/mdtraj.formats.HDF5TrajectoryFile writing output... [ 36%] api/generated/mdtraj.formats.LAMMPSTrajectoryFile writing output... [ 37%] api/generated/mdtraj.formats.LH5TrajectoryFile writing output... [ 37%] api/generated/mdtraj.formats.MDCRDTrajectoryFile writing output... [ 38%] api/generated/mdtraj.formats.NetCDFTrajectoryFile writing output... [ 39%] api/generated/mdtraj.formats.PDBTrajectoryFile writing output... [ 40%] api/generated/mdtraj.formats.TRRTrajectoryFile writing output... [ 40%] api/generated/mdtraj.formats.XTCTrajectoryFile writing output... [ 41%] api/generated/mdtraj.formats.XYZTrajectoryFile writing output... [ 42%] api/generated/mdtraj.geometry.squareform writing output... [ 43%] api/generated/mdtraj.isothermal_compressability_kappa_T writing output... [ 44%] api/generated/mdtraj.iterload writing output... [ 44%] api/generated/mdtraj.join writing output... [ 45%] api/generated/mdtraj.kabsch_sander writing output... [ 46%] api/generated/mdtraj.load writing output... [ 47%] api/generated/mdtraj.load_arc writing output... [ 48%] api/generated/mdtraj.load_binpos writing output... [ 48%] api/generated/mdtraj.load_dcd writing output... [ 49%] api/generated/mdtraj.load_dtr writing output... [ 50%] api/generated/mdtraj.load_frame writing output... [ 51%] api/generated/mdtraj.load_hdf5 writing output... [ 51%] api/generated/mdtraj.load_hoomdxml writing output... [ 52%] api/generated/mdtraj.load_lammpstrj writing output... [ 53%] api/generated/mdtraj.load_lh5 writing output... [ 54%] api/generated/mdtraj.load_netcdf writing output... [ 55%] api/generated/mdtraj.load_pdb writing output... [ 55%] api/generated/mdtraj.load_prmtop writing output... [ 56%] api/generated/mdtraj.load_trr writing output... [ 57%] api/generated/mdtraj.load_xml writing output... [ 58%] api/generated/mdtraj.load_xtc writing output... [ 59%] api/generated/mdtraj.load_xyz writing output... [ 59%] api/generated/mdtraj.lprmsd writing output... [ 60%] api/generated/mdtraj.open writing output... [ 61%] api/generated/mdtraj.principal_moments writing output... [ 62%] api/generated/mdtraj.reindex_dataframe_by_atoms writing output... [ 62%] api/generated/mdtraj.relative_shape_antisotropy writing output... [ 63%] api/generated/mdtraj.reporters.DCDReporter writing output... [ 64%] api/generated/mdtraj.reporters.HDF5Reporter writing output... [ 65%] api/generated/mdtraj.reporters.NetCDFReporter writing output... [ 66%] api/generated/mdtraj.rmsd writing output... [ 66%] api/generated/mdtraj.rmsf writing output... [ 67%] api/generated/mdtraj.shrake_rupley writing output... [ 68%] api/generated/mdtraj.static_dielectric writing output... [ 69%] api/generated/mdtraj.thermal_expansion_alpha_P writing output... [ 70%] api/generated/mdtraj.utils.box_vectors_to_lengths_and_angles writing output... [ 70%] api/generated/mdtraj.utils.check_random_state writing output... [ 71%] api/generated/mdtraj.utils.ensure_type writing output... [ 72%] api/generated/mdtraj.utils.ilen writing output... [ 73%] api/generated/mdtraj.utils.import_ writing output... [ 74%] api/generated/mdtraj.utils.in_units_of writing output... [ 74%] api/generated/mdtraj.utils.lengths_and_angles_to_box_vectors writing output... [ 75%] api/generated/mdtraj.utils.rotation_matrix_from_quaternion writing output... [ 76%] api/generated/mdtraj.utils.timing writing output... [ 77%] api/generated/mdtraj.utils.uniform_quaternion writing output... [ 77%] api/generated/mdtraj.wernet_nilsson writing output... [ 78%] api/reporters writing output... [ 79%] api/trajectory_files writing output... [ 80%] api/utils writing output... [ 81%] atom_selection writing output... [ 81%] building_docs writing output... [ 82%] examples/atom-selection writing output... [ 83%] examples/centroids writing output... [ 84%] examples/clustering writing output... [ 85%] examples/hbonds writing output... [ 85%] examples/index writing output... [ 86%] examples/introduction writing output... [ 87%] examples/iterload writing output... [ 88%] examples/native-contact writing output... [ 88%] examples/nmr writing output... [ 89%] examples/openmm writing output... [ 90%] examples/pca writing output... [ 91%] examples/ramachandran-plot writing output... [ 92%] examples/rmsd-benchmark writing output... [ 92%] examples/solvent-accessible-surface-area writing output... [ 93%] examples/two-pass-clustering writing output... [ 94%] faq writing output... [ 95%] hdf5_format writing output... [ 96%] index writing output... [ 96%] installation writing output... [ 97%] load_functions writing output... [ 98%] mdconvert writing output... [ 99%] new_to_python writing output... [100%] whatsnew generating indices... genindex done writing additional pages... search done copying static files... done copying extra files... done dumping search index in English (code: en)... done dumping object inventory... done build succeeded, 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/i686-linux-gnu-gcc COLLECT_LTO_WRAPPER=/usr/lib/gcc/i686-linux-gnu/10/lto-wrapper Target: i686-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=i686-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-targets=all --enable-multiarch --disable-werror --with-arch-32=i686 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-checking=release --build=i686-linux-gnu --host=i686-linux-gnu --target=i686-linux-gnu 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 0.000s OK create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary --with python3,sphinxdoc --buildsystem=pybuild dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_installdirs -O--buildsystem=pybuild dh_auto_install -O--buildsystem=pybuild I: pybuild base: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/i686-linux-gnu-gcc COLLECT_LTO_WRAPPER=/usr/lib/gcc/i686-linux-gnu/10/lto-wrapper Target: i686-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=i686-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-targets=all --enable-multiarch --disable-werror --with-arch-32=i686 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-checking=release --build=i686-linux-gnu --host=i686-linux-gnu --target=i686-linux-gnu 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 creating /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/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/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/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/__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/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/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__/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__/__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/__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/io.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/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/core 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/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/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/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/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/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/__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/residue_names.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/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__/__init__.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__/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__/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__/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/selection.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 creating /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/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/__init__.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/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__/__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/__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__/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/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/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/__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/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/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/__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__/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/__init__.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/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/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/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/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/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/__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 creating /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/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_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/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/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/__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/prefix.py -> /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__/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__/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__/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__/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__/__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/__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.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__/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__/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/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/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/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/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/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/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/delay_import.py -> /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__/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__/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__/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__/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__/__init__.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__/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__/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__/validation.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/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/binpos.cpython-39-i386-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-i386-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/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/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/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/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/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/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/xtc.cpython-39-i386-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/__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/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/dtr.cpython-39-i386-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/__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__/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__/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__/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/__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__/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__/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__/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__/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__/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__/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__/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__/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__/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__/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/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/xyzfile.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/trr.cpython-39-i386-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 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/pdb/__init__.py -> /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/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/data/pdbNames.xml -> /build/reproducible-path/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/pdb/data 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__/__init__.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__/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/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/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/tng.cpython-39-i386-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/hdf5.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 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/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/drid.cpython-39-i386-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-i386-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/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/neighborlist.cpython-39-i386-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/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/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/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/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/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/__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/thermodynamic_properties.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/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/_geometry.cpython-39-i386-linux-gnu.so -> /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__/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__/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__/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__/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__/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__/__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/__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__/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__/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__/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__/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__/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__/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/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/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/sasa.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/__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/__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/_lprmsd.cpython-39-i386-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-i386-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/scripts 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 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/mdinspect.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 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/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/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/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/__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/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/io.py to io.cpython-39.pyc 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/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/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/__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/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/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/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/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/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/__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/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/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/__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/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/__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/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/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/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/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/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/__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/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/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_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/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/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/__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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/__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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/__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/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/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/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/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/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/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/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/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/scripts/mdconvert.py to mdconvert.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 python-mdtraj-doc: substitution variable ${sphinxdoc:Built-Using} 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 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_i386.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_i386.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../mdtraj_1.9.5-1_i386.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: 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/104979 and its subdirectories I: Current time: Fri Feb 7 17:10:37 -12 2025 I: pbuilder-time-stamp: 1738991437 Sat Jan 6 22:47:40 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos12-i386.debian.net. Sat Jan 6 22:47:40 UTC 2024 I: Preparing to do remote build '2' on ionos12-i386.debian.net. Sat Jan 6 23:07:22 UTC 2024 I: Deleting $TMPDIR on ionos12-i386.debian.net. Sat Jan 6 23:07:23 UTC 2024 I: mdtraj_1.9.5-1_i386.changes: Format: 1.8 Date: Mon, 18 Jan 2021 16:30:54 +1100 Source: mdtraj Binary: python-mdtraj-doc python3-mdtraj python3-mdtraj-dbgsym Architecture: all i386 Version: 1.9.5-1 Distribution: unstable Urgency: medium Maintainer: Debichem Team Changed-By: Drew Parsons Description: python-mdtraj-doc - Read, write and analyze MD trajectories in Python (documentation) python3-mdtraj - Read, write and analyze MD trajectories in Python Closes: 980050 Changes: mdtraj (1.9.5-1) unstable; urgency=medium . * New upstream release. * Standards-Version: 4.5.1 * debian/tests: skip nmr.ipynb, it requires SPARTA+ which is not available. Closes: #980050. Checksums-Sha1: 99ae62f9fdbc7a823c1dde2dd8ad4282bdbb23f0 10681 mdtraj_1.9.5-1_i386.buildinfo d7e04dc632b3b4a4c530d56661b25cc40e6462cb 866872 python-mdtraj-doc_1.9.5-1_all.deb cd3a3499a023344aa1c03e5f9905572f9d0657c5 4943048 python3-mdtraj-dbgsym_1.9.5-1_i386.deb 51eadb599c659199b4aaa4745fb110121e22c058 1043356 python3-mdtraj_1.9.5-1_i386.deb Checksums-Sha256: ba0b05b5a7f35a1e20f01872e8d9237d7080e6687d897e6199ae944617c40819 10681 mdtraj_1.9.5-1_i386.buildinfo f9627903e47211e4acf57494fa6ca0a068bd2b8ebc95a3d0a99dc8cdb93b340e 866872 python-mdtraj-doc_1.9.5-1_all.deb a748699002e417f60249bbb5cf9473c8ffa4ca5f4c03779bd0c88f97cea80c71 4943048 python3-mdtraj-dbgsym_1.9.5-1_i386.deb c80e2d8022e170ac6893d5ff8fe7765cb3d9ec87923dcc72b361257e3a68016f 1043356 python3-mdtraj_1.9.5-1_i386.deb Files: 5f2a53b495b699f3df1f57b770385be3 10681 python optional mdtraj_1.9.5-1_i386.buildinfo 91cacc711686babbd03754b8d224bbe4 866872 doc optional python-mdtraj-doc_1.9.5-1_all.deb 36104f0ca40aa93b853989b47c511276 4943048 debug optional python3-mdtraj-dbgsym_1.9.5-1_i386.deb dd588976cb41af329df97a5617d6e476 1043356 python optional python3-mdtraj_1.9.5-1_i386.deb Sat Jan 6 23:07:24 UTC 2024 I: diffoscope 240 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.UfSHoaZj/mdtraj_1.9.5-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.UfSHoaZj/mdtraj_1.9.5-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.UfSHoaZj/mdtraj_1.9.5-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.UfSHoaZj/b1/mdtraj_1.9.5-1_i386.changes /srv/reproducible-results/rbuild-debian/r-b-build.UfSHoaZj/b2/mdtraj_1.9.5-1_i386.changes ## close_archive (total time: 0.001s) 0.000s 48 calls diffoscope.comparators.xz.XzContainer 0.000s 30 calls diffoscope.comparators.deb.DebTarContainer 0.000s 18 calls diffoscope.comparators.tar.TarContainer 0.000s 12 calls diffoscope.comparators.deb.DebContainer ## command (total time: 426.538s) 175.298s 12434 calls readelf 167.208s 1393 calls diff 66.214s 2535 calls objdump 8.100s 24 calls objcopy 6.372s 48 calls xz 1.971s 275 calls strings 0.896s 2 calls convert 0.157s 2 calls compare 0.113s 11 calls js-beautify 0.071s 4 calls identify 0.068s 20 calls sng 0.022s 33 calls html2text 0.021s 6 calls cmp 0.021s 6 calls cmp (external) 0.006s 65 calls cmp (internal) ## compare_files (cumulative) (total time: 1191.635s) 223.919s 1 call abc.DotChangesFile 223.894s 3 calls abc.DebFile 223.773s 6 calls abc.XzFile 222.524s 3 calls abc.DebDataTarFile 217.289s 25 calls abc.ElfFile 68.186s 120 calls diffoscope.comparators.elf.ElfCodeSection 7.101s 421 calls diffoscope.comparators.elf.ElfSection 2.108s 1 call abc.JavaScriptFile 1.510s 2 calls abc.PngFile 0.694s 25 calls diffoscope.comparators.elf.ElfStringSection 0.227s 12 calls diffoscope.comparators.elf.MonkeyPatchedElfSection 0.186s 3 calls abc.HtmlFile 0.160s 3 calls abc.TarFile 0.033s 2 calls abc.TextFile 0.029s 3 calls abc.Md5sumsFile ## container_extract (total time: 7.229s) 6.374s 48 calls diffoscope.comparators.xz.XzContainer 0.733s 960 calls diffoscope.comparators.deb.DebTarContainer 0.098s 54 calls diffoscope.comparators.deb.DebContainer 0.023s 28 calls diffoscope.comparators.tar.TarContainer ## diff (total time: 6.806s) 6.806s 1192 calls linediff ## has_same_content_as (total time: 0.037s) 0.013s 25 calls abc.ElfFile 0.012s 3 calls abc.DebDataTarFile 0.003s 24 calls diffoscope.comparators.utils.libarchive.LibarchiveSymlink 0.003s 421 calls diffoscope.comparators.elf.ElfSection 0.001s 8 calls abc.TextFile 0.001s 3 calls abc.HtmlFile 0.001s 6 calls abc.Md5sumsFile 0.001s 120 calls diffoscope.comparators.elf.ElfCodeSection 0.001s 6 calls abc.XzFile 0.000s 3 calls abc.TarFile 0.000s 3 calls abc.DebFile 0.000s 1 call abc.JavaScriptFile 0.000s 25 calls diffoscope.comparators.elf.ElfStringSection 0.000s 1 call abc.DotChangesFile 0.000s 2 calls abc.PngFile 0.000s 12 calls diffoscope.comparators.elf.MonkeyPatchedElfSection ## main (total time: 1796.883s) 1796.880s 2 calls outputs 0.003s 1 call cleanup ## open_archive (total time: 0.001s) 0.000s 48 calls diffoscope.comparators.xz.XzContainer 0.000s 30 calls diffoscope.comparators.deb.DebTarContainer 0.000s 18 calls diffoscope.comparators.tar.TarContainer 0.000s 12 calls diffoscope.comparators.deb.DebContainer ## output (total time: 1572.519s) 1569.781s 1 call html 1.684s 1 call text 1.054s 1 call json ## recognizes (total time: 7.647s) 5.537s 1362 calls diffoscope.comparators.utils.archive.ArchiveMember 0.937s 6116 calls diffoscope.comparators.utils.libarchive.LibarchiveMember 0.757s 9262 calls diffoscope.comparators.elf.ElfSection 0.226s 2640 calls diffoscope.comparators.elf.ElfCodeSection 0.100s 12 calls diffoscope.comparators.binary.FilesystemFile 0.043s 550 calls diffoscope.comparators.elf.ElfStringSection 0.033s 324 calls diffoscope.comparators.debian.DebControlMember 0.012s 264 calls diffoscope.comparators.elf.MonkeyPatchedElfSection 0.001s 96 calls diffoscope.comparators.utils.libarchive.LibarchiveSymlink 0.001s 48 calls abc.Md5sumsFile 0.000s 10 calls abc.DotChangesFile ## specialize (total time: 1.458s) 1.458s 663 calls specialize Sat Jan 6 23:37:21 UTC 2024 E: mdtraj failed to build reproducibly in bullseye on i386. Sat Jan 6 23:37:21 UTC 2024 E: diffoscope 240 found issues, please check https://tests.reproducible-builds.org/debian/dbd/bullseye/i386/mdtraj_1.9.5-1.diffoscope.html Sat Jan 6 23:37:58 UTC 2024 I: Submitting .buildinfo files to external archives: Sat Jan 6 23:37:58 UTC 2024 I: Submitting 12K b1/mdtraj_1.9.5-1_i386.buildinfo.asc Sat Jan 6 23:37:59 UTC 2024 I: Submitting 12K b2/mdtraj_1.9.5-1_i386.buildinfo.asc Sat Jan 6 23:38:00 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sat Jan 6 23:38:00 UTC 2024 I: Done submitting .buildinfo files. Sat Jan 6 23:38:00 UTC 2024 I: Removing signed mdtraj_1.9.5-1_i386.buildinfo.asc files: removed './b1/mdtraj_1.9.5-1_i386.buildinfo.asc' removed './b2/mdtraj_1.9.5-1_i386.buildinfo.asc'