Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/m/mdtraj/mdtraj_1.9.7-3_all.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/mdtraj-1.9.7-355jgahh0/mdtraj_1.9.7-3_all.buildinfo Get source package info: mdtraj=1.9.7-3 Source URL: http://snapshot.notset.fr/mr/package/mdtraj/1.9.7-3/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=autoconf=2.71-2 automake=1:1.16.5-1.3 autopoint=0.21-6 autotools-dev=20220109.1 base-files=12.2 base-passwd=3.5.52 bash=5.1-6 binutils=2.38-3 binutils-common=2.38-3 binutils-x86-64-linux-gnu=2.38-3 blt=2.5.3+dfsg-4.1 bsdextrautils=2.37.3-1+b1 bsdutils=1:2.37.3-1+b1 build-essential=12.9 bzip2=1.0.8-5 ca-certificates=20211016 coreutils=8.32-4.1 cpp=4:11.2.0-2 cpp-11=11.2.0-19 cython3=0.29.28-3 dash=0.5.11+git20210903+057cd650a4ed-8 debconf=1.5.79 debhelper=13.6 debianutils=5.7-0.1 dh-autoreconf=20 dh-python=5.20220215 dh-strip-nondeterminism=1.13.0-1 diffutils=1:3.7-5 docutils-common=0.17.1+dfsg-2 dpkg=1.21.6 dpkg-dev=1.21.6 dwz=0.14-1 file=1:5.41-3 findutils=4.9.0-2 fontconfig-config=2.13.1-4.4 fonts-dejavu-core=2.37-2 fonts-font-awesome=5.0.10+really4.7.0~dfsg-4.1 fonts-lato=2.0-2.1 fonts-lyx=2.3.6-1 fonts-mathjax=2.7.9+dfsg-1 g++=4:11.2.0-2 g++-11=11.2.0-19 gcc=4:11.2.0-2 gcc-11=11.2.0-19 gcc-11-base=11.2.0-19 gcc-12-base=12-20220319-1 gettext=0.21-6 gettext-base=0.21-6 grep=3.7-1 groff-base=1.22.4-8 gzip=1.10-4 hostname=3.23 init-system-helpers=1.62 intltool-debian=0.35.0+20060710.5 libacl1=2.3.1-1 libaec0=1.0.6-1 libarchive-zip-perl=1.68-1 libasan6=11.2.0-19 libatomic1=12-20220319-1 libattr1=1:2.5.1-1 libaudit-common=1:3.0.7-1 libaudit1=1:3.0.7-1+b1 libbinutils=2.38-3 libblas3=3.10.0-2 libblkid1=2.37.3-1+b1 libblosc1=1.21.1+ds2-2 libbrotli1=1.0.9-2+b3 libbsd0=0.11.6-1 libbz2-1.0=1.0.8-5 libc-bin=2.33-7 libc-dev-bin=2.33-7 libc6=2.33-7 libc6-dev=2.33-7 libcap-ng0=0.7.9-2.2+b2 libcap2=1:2.44-1 libcc1-0=12-20220319-1 libcom-err2=1.46.5-2 libcrypt-dev=1:4.4.27-1.1 libcrypt1=1:4.4.27-1.1 libctf-nobfd0=2.38-3 libctf0=2.38-3 libcurl4=7.82.0-2 libdb5.3=5.3.28+dfsg1-0.8 libdebconfclient0=0.261 libdebhelper-perl=13.6 libdeflate0=1.10-2 libdpkg-perl=1.21.6 libelf1=0.186-1 libexpat1=2.4.8-1 libexpat1-dev=2.4.8-1 libffi8=3.4.2-4 libfile-stripnondeterminism-perl=1.13.0-1 libfontconfig1=2.13.1-4.4 libfreetype6=2.11.1+dfsg-1 libfribidi0=1.0.8-2 libgcc-11-dev=11.2.0-19 libgcc-s1=12-20220319-1 libgcrypt20=1.9.4-5 libgdbm-compat4=1.23-1 libgdbm6=1.23-1 libgfortran5=12-20220319-1 libglib2.0-0=2.72.0-1+b1 libgmp10=2:6.2.1+dfsg-3 libgnutls30=3.7.3-4+b1 libgomp1=12-20220319-1 libgpg-error0=1.43-3 libgraphite2-3=1.3.14-1 libgssapi-krb5-2=1.19.2-2+b1 libharfbuzz0b=2.7.4-1 libhdf5-103-1=1.10.7+repack-4 libhogweed6=3.7.3-1 libicu67=67.1-7 libidn2-0=2.3.2-2 libimagequant0=2.17.0-1 libisl23=0.24-2 libitm1=12-20220319-1 libjbig0=2.1-3.1+b2 libjpeg62-turbo=1:2.1.2-1 libjs-jquery=3.6.0+dfsg+~3.5.13-1 libjs-jquery-ui=1.13.1+dfsg-1 libjs-mathjax=2.7.9+dfsg-1 libjs-sphinxdoc=4.5.0-1 libjs-underscore=1.13.2~dfsg-2 libk5crypto3=1.19.2-2+b1 libkeyutils1=1.6.1-3 libkrb5-3=1.19.2-2+b1 libkrb5support0=1.19.2-2+b1 liblapack3=3.10.0-2 liblbfgsb0=3.0+dfsg.3-10 liblcms2-2=2.12~rc1-2 libldap-2.5-0=2.5.11+dfsg-1 liblsan0=12-20220319-1 liblz4-1=1.9.3-2 liblzma5=5.2.5-2 liblzo2-2=2.10-2 libmagic-mgc=1:5.41-3 libmagic1=1:5.41-3 libmd0=1.0.4-1 libmount1=2.37.3-1+b1 libmpc3=1.2.1-2 libmpdec3=2.5.1-2 libmpfr6=4.1.0-3 libncurses6=6.3-2 libncursesw6=6.3-2 libnettle8=3.7.3-1 libnghttp2-14=1.43.0-1 libnorm1=1.5.9+dfsg-2 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libopenjp2-7=2.4.0-6 libp11-kit0=0.24.0-6 libpam-modules=1.4.0-11 libpam-modules-bin=1.4.0-11 libpam-runtime=1.4.0-11 libpam0g=1.4.0-11 libpcre2-8-0=10.39-3 libpcre3=2:8.39-13 libperl5.34=5.34.0-3 libpgm-5.3-0=5.3.128~dfsg-2 libpipeline1=1.5.5-1 libpng16-16=1.6.37-3 libprocps8=2:3.3.17-7+b1 libpsl5=0.21.0-1.2 libpython3-all-dev=3.10.4-1 libpython3-dev=3.10.4-1 libpython3-stdlib=3.10.4-1 libpython3.10=3.10.4-2 libpython3.10-dev=3.10.4-2 libpython3.10-minimal=3.10.4-2 libpython3.10-stdlib=3.10.4-2 libpython3.9=3.9.12-1 libpython3.9-dev=3.9.12-1 libpython3.9-minimal=3.9.12-1 libpython3.9-stdlib=3.9.12-1 libqhull-r8.0=2020.2-4 libquadmath0=12-20220319-1 libraqm0=0.7.0-4 libreadline8=8.1.2-1 librtmp1=2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2=2.1.28+dfsg-2+b1 libsasl2-modules-db=2.1.28+dfsg-2+b1 libseccomp2=2.5.3-2 libselinux1=3.3-1+b2 libsigsegv2=2.14-1 libsmartcols1=2.37.3-1+b1 libsnappy1v5=1.1.8-1 libsodium23=1.0.18-1 libsqlite3-0=3.38.2-1 libssh2-1=1.10.0-3 libssl1.1=1.1.1n-1 libstdc++-11-dev=11.2.0-19 libstdc++6=12-20220319-1 libsub-override-perl=0.09-2 libsystemd0=250.4-1 libsz2=1.0.6-1 libtasn1-6=4.18.0-4 libtcl8.6=8.6.12+dfsg-1 libtiff5=4.3.0-6 libtinfo6=6.3-2 libtirpc-common=1.3.2-2 libtirpc-dev=1.3.2-2 libtirpc3=1.3.2-2 libtk8.6=8.6.12-1 libtool=2.4.7-2 libtsan0=11.2.0-19 libubsan1=12-20220319-1 libuchardet0=0.0.7-1 libudev1=250.4-1 libunicode-escape-perl=0.0.2-4.1 libunicode-string-perl=2.10-1+b7 libunistring2=1.0-1 libuuid1=2.37.3-1+b1 libwebp7=1.2.2-2+b1 libwebpdemux2=1.2.2-2+b1 libwebpmux3=1.2.2-2+b1 libx11-6=2:1.7.4-1 libx11-data=2:1.7.4-1 libxau6=1:1.0.9-1 libxcb1=1.14-3 libxdmcp6=1:1.1.2-3 libxext6=2:1.3.4-1 libxft2=2.3.4-1 libxml2=2.9.13+dfsg-1 libxrender1=1:0.9.10-1 libxslt1.1=1.1.34-4 libxss1=1:1.2.3-1 libzmq5=4.3.4-2 libzstd1=1.4.9+dfsg-1 linux-libc-dev=5.16.18-1 login=1:4.11.1+dfsg1-2 lsb-base=11.1.0 m4=1.4.18-5 make=4.3-4.1 man-db=2.10.2-1 mawk=1.3.4.20200120-3+b1 media-types=7.0.0 ncurses-base=6.3-2 ncurses-bin=6.3-2 openssl=1.1.1n-1 patch=2.7.6-7 perl=5.34.0-3 perl-base=5.34.0-3 perl-modules-5.34=5.34.0-3 po-debconf=1.0.21+nmu1 procps=2:3.3.17-7+b1 python-babel-localedata=2.8.0+dfsg.1-7 python-matplotlib-data=3.5.1-2 python-tables-data=3.7.0-2 python3=3.10.4-1 python3-alabaster=0.7.12-1 python3-all=3.10.4-1 python3-all-dev=3.10.4-1 python3-appdirs=1.4.4-2 python3-astunparse=1.6.3-1 python3-attr=21.2.0-1 python3-babel=2.8.0+dfsg.1-7 python3-backcall=0.2.0-3 python3-bleach=4.1.0-1 python3-brotli=1.0.9-2+b3 python3-bs4=4.10.0-2 python3-certifi=2020.6.20-1 python3-chardet=4.0.0-1 python3-charset-normalizer=2.0.6-2 python3-cycler=0.11.0-1 python3-dateutil=2.8.1-6 python3-decorator=4.4.2-2 python3-defusedxml=0.7.1-1 python3-dev=3.10.4-1 python3-distutils=3.9.12-1 python3-docutils=0.17.1+dfsg-2 python3-entrypoints=0.4-1 python3-fonttools=4.29.1-2 python3-fs=2.4.12-1 python3-html5lib=1.1-3 python3-idna=3.3-1 python3-imagesize=1.3.0-1 python3-ipykernel=6.9.2-1 python3-ipython=7.31.1-1 python3-jedi=0.18.0-1 python3-jinja2=3.0.3-1 python3-joblib=0.17.0-4 python3-jsonschema=3.2.0-5 python3-jupyter-client=7.1.2-1 python3-jupyter-core=4.9.2-1 python3-jupyterlab-pygments=0.1.2-8 python3-kiwisolver=1.3.2-1+b1 python3-lib2to3=3.9.12-1 python3-lxml=4.8.0-1 python3-lz4=4.0.0+dfsg-1 python3-markupsafe=2.0.1-2+b1 python3-matplotlib=3.5.1-2+b1 python3-matplotlib-inline=0.1.3-1 python3-minimal=3.10.4-1 python3-mpmath=1.2.1-2 python3-msmb-theme=1.2.0-2 python3-nbclient=0.5.13-1 python3-nbconvert=6.4.4-1 python3-nbformat=5.2.0-1 python3-nest-asyncio=1.5.4-1 python3-networkx=2.5+ds-2 python3-numexpr=2.8.1-1 python3-numpy=1:1.21.5-1 python3-numpydoc=1.2.1-1 python3-packaging=21.3-1 python3-pandas=1.3.5+dfsg-3 python3-pandas-lib=1.3.5+dfsg-3 python3-pandocfilters=1.5.0-1 python3-parso=0.8.1-1 python3-pexpect=4.8.0-2 python3-pickleshare=0.7.5-5 python3-pil=9.0.1-1 python3-pil.imagetk=9.0.1-1 python3-pkg-resources=59.6.0-1.2 python3-prompt-toolkit=3.0.28-1 python3-psutil=5.9.0-1 python3-ptyprocess=0.7.0-3 python3-pygments=2.11.2+dfsg-2 python3-pyparsing=3.0.7-1 python3-pyrsistent=0.18.1-1 python3-requests=2.27.1+dfsg-1 python3-roman=3.3-1 python3-scipy=1.7.3-2 python3-setuptools=59.6.0-1.2 python3-six=1.16.0-3 python3-sklearn=1.0.2-1 python3-sklearn-lib=1.0.2-1 python3-snowballstemmer=2.2.0-1 python3-soupsieve=2.3.1-1 python3-sphinx=4.5.0-1 python3-sphinx-rtd-theme=1.0.0+dfsg-1 python3-sympy=1.9-1 python3-tables=3.7.0-2 python3-tables-lib=3.7.0-2 python3-testpath=0.6.0+dfsg-1 python3-threadpoolctl=3.1.0-1 python3-tk=3.9.12-1 python3-tornado=6.1.0-3 python3-traitlets=5.1.1-1 python3-tz=2022.1-1 python3-ufolib2=0.13.1+dfsg1-1 python3-unicodedata2=14.0.0+ds-8 python3-urllib3=1.26.9-1 python3-wcwidth=0.2.5+dfsg1-1 python3-webencodings=0.5.1-4 python3-zmq=22.3.0-1+b1 python3.10=3.10.4-2 python3.10-dev=3.10.4-2 python3.10-minimal=3.10.4-2 python3.9=3.9.12-1 python3.9-dev=3.9.12-1 python3.9-minimal=3.9.12-1 readline-common=8.1.2-1 rpcsvc-proto=1.4.2-4 sed=4.8-1 sensible-utils=0.0.17 sgml-base=1.30 sphinx-common=4.5.0-1 sphinx-rtd-theme-common=1.0.0+dfsg-1 sysvinit-utils=3.01-1 tar=1.34+dfsg-1 tk8.6-blt2.5=2.5.3+dfsg-4.1 tzdata=2022a-1 ucf=3.0043 unicode-data=14.0.0-1.1 util-linux=2.37.3-1+b1 x11-common=1:7.7+23 xml-core=0.18+nmu1 xz-utils=5.2.5-2 zlib1g=1:1.2.11.dfsg-4 zlib1g-dev=1:1.2.11.dfsg-4 --variant=apt --aptopt=Acquire::Check-Valid-Until "false" --aptopt=Acquire::http::Dl-Limit "1000"; --aptopt=Acquire::https::Dl-Limit "1000"; --aptopt=Acquire::Retries "5"; --aptopt=APT::Get::allow-downgrades "true"; --keyring=/usr/share/keyrings/ --essential-hook=chroot "$1" sh -c "apt-get --yes install fakeroot util-linux" --essential-hook=copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ --essential-hook=chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20220409T024953Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20220409T024953Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20220422T145207Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20220403T085258Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20220331T214746Z/ unstable main' >> /etc/apt/sources.list && apt-get update" --customize-hook=chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash --customize-hook=chroot "$1" env sh -c "apt-get source --only-source -d mdtraj=1.9.7-3 && mkdir -p /build/mdtraj-X0NYWR && dpkg-source --no-check -x /*.dsc /build/mdtraj-X0NYWR/mdtraj-1.9.7 && chown -R builduser:builduser /build/mdtraj-X0NYWR" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/mdtraj-X0NYWR/mdtraj-1.9.7 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1649004107" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=all" --customize-hook=sync-out /build/mdtraj-X0NYWR /tmp/mdtraj-1.9.7-355jgahh0 bookworm /dev/null deb http://snapshot.notset.fr/archive/debian/20220331T214746Z unstable main I: automatically chosen mode: root I: chroot architecture amd64 is equal to the host's architecture I: automatically chosen format: null I: using /tmp/mmdebstrap.r2iyty6Saz as tempdir I: running apt-get update... I: downloading packages with apt... I: extracting archives... I: installing essential packages... I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "apt-get --yes install fakeroot util-linux"' exec /tmp/mmdebstrap.r2iyty6Saz Reading package lists... Building dependency tree... util-linux is already the newest version (2.37.3-1+b1). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 135 kB of archives. After this operation, 406 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20220331T214746Z unstable/main amd64 libfakeroot amd64 1.28-1 [48.2 kB] Get:2 http://snapshot.notset.fr/archive/debian/20220331T214746Z unstable/main amd64 fakeroot amd64 1.28-1 [87.2 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 135 kB in 0s (1030 kB/s) Selecting previously unselected package libfakeroot:amd64. (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 ... 4702 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.28-1_amd64.deb ... Unpacking libfakeroot:amd64 (1.28-1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.28-1_amd64.deb ... Unpacking fakeroot (1.28-1) ... Setting up libfakeroot:amd64 (1.28-1) ... Setting up fakeroot (1.28-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.33-7) ... I: running special hook: copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20220409T024953Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20220409T024953Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20220422T145207Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20220403T085258Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20220331T214746Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.r2iyty6Saz Get:1 http://snapshot.notset.fr/archive/debian/20220409T024953Z bookworm InRelease [130 kB] Get:2 http://snapshot.notset.fr/archive/debian/20220422T145207Z unstable InRelease [165 kB] Get:3 http://snapshot.notset.fr/archive/debian/20220403T085258Z unstable InRelease [165 kB] Hit:4 http://snapshot.notset.fr/archive/debian/20220331T214746Z unstable InRelease Ign:5 http://snapshot.notset.fr/archive/debian/20220409T024953Z bookworm/main Sources Ign:6 http://snapshot.notset.fr/archive/debian/20220409T024953Z bookworm/main amd64 Packages Ign:5 http://snapshot.notset.fr/archive/debian/20220409T024953Z bookworm/main Sources Ign:6 http://snapshot.notset.fr/archive/debian/20220409T024953Z bookworm/main amd64 Packages Ign:5 http://snapshot.notset.fr/archive/debian/20220409T024953Z bookworm/main Sources Ign:6 http://snapshot.notset.fr/archive/debian/20220409T024953Z bookworm/main amd64 Packages Get:5 http://snapshot.notset.fr/archive/debian/20220409T024953Z bookworm/main Sources [12.0 MB] Get:6 http://snapshot.notset.fr/archive/debian/20220409T024953Z bookworm/main amd64 Packages [11.4 MB] Ign:7 http://snapshot.notset.fr/archive/debian/20220422T145207Z unstable/main amd64 Packages Ign:8 http://snapshot.notset.fr/archive/debian/20220403T085258Z unstable/main amd64 Packages Ign:7 http://snapshot.notset.fr/archive/debian/20220422T145207Z unstable/main amd64 Packages Ign:8 http://snapshot.notset.fr/archive/debian/20220403T085258Z unstable/main amd64 Packages Ign:7 http://snapshot.notset.fr/archive/debian/20220422T145207Z unstable/main amd64 Packages Ign:8 http://snapshot.notset.fr/archive/debian/20220403T085258Z unstable/main amd64 Packages Get:7 http://snapshot.notset.fr/archive/debian/20220422T145207Z unstable/main amd64 Packages [12.4 MB] Get:8 http://snapshot.notset.fr/archive/debian/20220403T085258Z unstable/main amd64 Packages [12.4 MB] Fetched 48.6 MB in 40s (1223 kB/s) Reading package lists... I: installing remaining packages inside the chroot... I: running --customize-hook in shell: sh -c 'chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash' exec /tmp/mmdebstrap.r2iyty6Saz I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d mdtraj=1.9.7-3 && mkdir -p /build/mdtraj-X0NYWR && dpkg-source --no-check -x /*.dsc /build/mdtraj-X0NYWR/mdtraj-1.9.7 && chown -R builduser:builduser /build/mdtraj-X0NYWR"' exec /tmp/mmdebstrap.r2iyty6Saz Reading package lists... NOTICE: 'mdtraj' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/debichem-team/mdtraj.git Please use: git clone https://salsa.debian.org/debichem-team/mdtraj.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 22.0 MB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20220409T024953Z bookworm/main mdtraj 1.9.7-3 (dsc) [2597 B] Get:2 http://snapshot.notset.fr/archive/debian/20220409T024953Z bookworm/main mdtraj 1.9.7-3 (tar) [21.7 MB] Get:3 http://snapshot.notset.fr/archive/debian/20220409T024953Z bookworm/main mdtraj 1.9.7-3 (diff) [296 kB] Fetched 22.0 MB in 17s (1282 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'mdtraj_1.9.7-3.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting mdtraj in /build/mdtraj-X0NYWR/mdtraj-1.9.7 dpkg-source: info: unpacking mdtraj_1.9.7.orig.tar.gz dpkg-source: info: unpacking mdtraj_1.9.7-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying docs_use_local_mathjax.patch dpkg-source: info: applying build_dir_pybuild.patch dpkg-source: info: applying python_hashbang.patch dpkg-source: info: applying test_gsd_skip.patch dpkg-source: info: applying check_sse2.patch dpkg-source: info: applying 32bit_skip_image_molecule.patch dpkg-source: info: applying test_relax_tol.patch dpkg-source: info: applying rename-mdconvert-mdtraj.patch dpkg-source: info: applying drop_notebook_in_docs.patch I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/mdtraj-X0NYWR/mdtraj-1.9.7 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1649004107" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=all"' exec /tmp/mmdebstrap.r2iyty6Saz dpkg-buildpackage: info: source package mdtraj dpkg-buildpackage: info: source version 1.9.7-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Drew Parsons dpkg-source --before-build . dpkg-source: info: using options from mdtraj-1.9.7/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/ fakeroot debian/rules clean dh clean --with python3,sphinxdoc --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/build/mdtraj-X0NYWR/mdtraj-1.9.7' dh_auto_clean || /bin/true I: pybuild base:237: python3.9 setup.py clean Using built-in specs. COLLECT_GCC=/usr/bin/x86_64-linux-gnu-gcc COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/11/lto-wrapper OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa OFFLOAD_TARGET_DEFAULT=1 Target: x86_64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 11.2.0-19' --with-bugurl=file:///usr/share/doc/gcc-11/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-11 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --enable-cet --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/gcc-11-uiwEqG/gcc-11-11.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-11-uiwEqG/gcc-11-11.2.0/debian/tmp-gcn/usr --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=2 Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 11.2.0 (Debian 11.2.0-19) /build/mdtraj-X0NYWR/mdtraj-1.9.7/./basesetup.py:431: UserWarning: Unrecognized setuptools command ('clean'), proceeding with generating Cython sources and expanding templates warnings.warn("Unrecognized setuptools command ('{}'), proceeding with " 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/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build' (and everything under it) 'build/bdist.linux-x86_64' does not exist -- can't clean it 'build/scripts-3.9' does not exist -- can't clean it I: pybuild base:237: python3.10 setup.py clean Using built-in specs. COLLECT_GCC=/usr/bin/x86_64-linux-gnu-gcc COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/11/lto-wrapper OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa OFFLOAD_TARGET_DEFAULT=1 Target: x86_64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 11.2.0-19' --with-bugurl=file:///usr/share/doc/gcc-11/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-11 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --enable-cet --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/gcc-11-uiwEqG/gcc-11-11.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-11-uiwEqG/gcc-11-11.2.0/debian/tmp-gcn/usr --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=2 Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 11.2.0 (Debian 11.2.0-19) /build/mdtraj-X0NYWR/mdtraj-1.9.7/./basesetup.py:431: UserWarning: Unrecognized setuptools command ('clean'), proceeding with generating Cython sources and expanding templates warnings.warn("Unrecognized setuptools command ('{}'), proceeding with " 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 clean removing '/build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build' (and everything under it) 'build/bdist.linux-x86_64' does not exist -- can't clean it 'build/scripts-3.10' does not exist -- can't clean it for f in mdtraj/formats/binpos/binpos.c \ mdtraj/formats/dcd/dcd.c \ mdtraj/formats/dtr/dtr.cpp \ mdtraj/formats/tng/tng.c \ mdtraj/formats/xtc/trr.c \ mdtraj/formats/xtc/xtc.c \ mdtraj/geometry/drid.cpp \ mdtraj/geometry/neighborlist.cpp \ mdtraj/geometry/neighbors.cpp \ mdtraj/geometry/src/_geometry.cpp \ mdtraj/rmsd/_lprmsd.cpp \ mdtraj/rmsd/_rmsd.cpp \ mdtraj/version.py; \ do rm -f $f; done rm -rf __pycache__ make[1]: Leaving directory '/build/mdtraj-X0NYWR/mdtraj-1.9.7' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules build-indep dh build-indep --with python3,sphinxdoc --buildsystem=pybuild dh_update_autotools_config -i -O--buildsystem=pybuild dh_autoreconf -i -O--buildsystem=pybuild dh_auto_configure -i -O--buildsystem=pybuild I: pybuild base:237: python3.9 setup.py config Using built-in specs. COLLECT_GCC=/usr/bin/x86_64-linux-gnu-gcc COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/11/lto-wrapper OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa OFFLOAD_TARGET_DEFAULT=1 Target: x86_64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 11.2.0-19' --with-bugurl=file:///usr/share/doc/gcc-11/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-11 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --enable-cet --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/gcc-11-uiwEqG/gcc-11-11.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-11-uiwEqG/gcc-11-11.2.0/debian/tmp-gcn/usr --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=2 Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 11.2.0 (Debian 11.2.0-19) /build/mdtraj-X0NYWR/mdtraj-1.9.7/./basesetup.py:431: UserWarning: Unrecognized setuptools command ('config'), proceeding with generating Cython sources and expanding templates warnings.warn("Unrecognized setuptools command ('{}'), proceeding with " 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 I: pybuild base:237: python3.10 setup.py config Using built-in specs. COLLECT_GCC=/usr/bin/x86_64-linux-gnu-gcc COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/11/lto-wrapper OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa OFFLOAD_TARGET_DEFAULT=1 Target: x86_64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 11.2.0-19' --with-bugurl=file:///usr/share/doc/gcc-11/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-11 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --enable-cet --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/gcc-11-uiwEqG/gcc-11-11.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-11-uiwEqG/gcc-11-11.2.0/debian/tmp-gcn/usr --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=2 Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 11.2.0 (Debian 11.2.0-19) /build/mdtraj-X0NYWR/mdtraj-1.9.7/./basesetup.py:431: UserWarning: Unrecognized setuptools command ('config'), proceeding with generating Cython sources and expanding templates warnings.warn("Unrecognized setuptools command ('{}'), proceeding with " 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 config debian/rules override_dh_auto_build-indep make[1]: Entering directory '/build/mdtraj-X0NYWR/mdtraj-1.9.7' dh_auto_build I: pybuild base:237: /usr/bin/python3.9 setup.py build Using built-in specs. COLLECT_GCC=/usr/bin/x86_64-linux-gnu-gcc COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/11/lto-wrapper OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa OFFLOAD_TARGET_DEFAULT=1 Target: x86_64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 11.2.0-19' --with-bugurl=file:///usr/share/doc/gcc-11/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-11 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --enable-cet --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/gcc-11-uiwEqG/gcc-11-11.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-11-uiwEqG/gcc-11-11.2.0/debian/tmp-gcn/usr --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=2 Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 11.2.0 (Debian 11.2.0-19) 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/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj copying mdtraj/__init__.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj copying mdtraj/io.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj copying mdtraj/version.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj creating /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/core copying mdtraj/core/__init__.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/core copying mdtraj/core/element.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/core copying mdtraj/core/residue_names.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/core copying mdtraj/core/selection.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/core copying mdtraj/core/topology.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/core copying mdtraj/core/trajectory.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/core creating /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats copying mdtraj/formats/__init__.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats copying mdtraj/formats/amberrst.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats copying mdtraj/formats/arc.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats copying mdtraj/formats/gro.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats copying mdtraj/formats/gsd.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats copying mdtraj/formats/hdf5.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats copying mdtraj/formats/hoomdxml.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats copying mdtraj/formats/lammpstrj.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats copying mdtraj/formats/lh5.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats copying mdtraj/formats/mdcrd.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats copying mdtraj/formats/mol2.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats copying mdtraj/formats/netcdf.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats copying mdtraj/formats/openmmxml.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats copying mdtraj/formats/prmtop.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats copying mdtraj/formats/psf.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats copying mdtraj/formats/registry.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats copying mdtraj/formats/xyzfile.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats creating /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/__init__.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/alignment.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/angle.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/contact.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/dihedral.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/distance.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/dssp.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/hbond.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/internal.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/order.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/rdf.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/rg.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/sasa.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/shape.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/thermodynamic_properties.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry creating /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/nmr copying mdtraj/nmr/__init__.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/nmr copying mdtraj/nmr/scalar_couplings.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/nmr copying mdtraj/nmr/shift_wrappers.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/nmr creating /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/__init__.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/basereporter.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/dcdreporter.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/hdf5reporter.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/netcdfreporter.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/xtcreporter.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/reporters creating /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/scripts copying mdtraj/scripts/__init__.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/scripts copying mdtraj/scripts/mdconvert.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/scripts copying mdtraj/scripts/mdinspect.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/scripts creating /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/testing copying mdtraj/testing/__init__.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/testing copying mdtraj/testing/docscrape.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/testing copying mdtraj/testing/docstrings.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/testing copying mdtraj/testing/testing.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/testing creating /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils copying mdtraj/utils/__init__.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils copying mdtraj/utils/contextmanagers.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils copying mdtraj/utils/delay_import.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils copying mdtraj/utils/rotation.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils copying mdtraj/utils/singleton.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils copying mdtraj/utils/six.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils copying mdtraj/utils/unitcell.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils copying mdtraj/utils/validation.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils copying mdtraj/utils/zipped.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils creating /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/pdb copying mdtraj/formats/pdb/__init__.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/pdb copying mdtraj/formats/pdb/pdbfile.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/pdb copying mdtraj/formats/pdb/pdbstructure.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/pdb creating /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/__init__.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/basedimension.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/baseunit.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/doctests.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/mymatrix.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/unit.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/constants.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/prefix.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/quantity.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/standard_dimensions.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/unit_definitions.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/unit_math.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/unit_operators.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit creating /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/pdb/data copying mdtraj/formats/pdb/data/pdbNames.xml -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/pdb/data copying mdtraj/formats/pdb/data/residues.xml -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/pdb/data running build_ext building 'mdtraj.formats.xtc' extension creating build creating build/temp.linux-x86_64-3.9 creating build/temp.linux-x86_64-3.9/mdtraj creating build/temp.linux-x86_64-3.9/mdtraj/formats creating build/temp.linux-x86_64-3.9/mdtraj/formats/xtc creating build/temp.linux-x86_64-3.9/mdtraj/formats/xtc/src x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/xtc/src/xdrfile.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_float’: mdtraj/formats/xtc/src/xdrfile.c:788:32: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 788 | int smallnum, smaller, larger, i, is_smaller, run; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c:785:23: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 785 | int smallidx, minidx, maxidx; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_float’: mdtraj/formats/xtc/src/xdrfile.c:1016:13: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable] 1016 | int errval=1; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_double’: mdtraj/formats/xtc/src/xdrfile.c:1305:32: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 1305 | int smallnum, smaller, larger, i, is_smaller, run; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c:1302:23: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 1302 | int smallidx, minidx, maxidx; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_double’: mdtraj/formats/xtc/src/xdrfile.c:1509:13: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable] 1509 | int errval=1; | ^~~~~~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/xtc/src/xdrfile_xtc.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/xtc/src/xdrfile_xtc.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/formats/xtc/src/xdrfile_xtc.c: In function ‘xtc_coord’: mdtraj/formats/xtc/src/xdrfile_xtc.c:66:15: warning: unused variable ‘j’ [-Wunused-variable] 66 | int i,j,result; | ^ mdtraj/formats/xtc/src/xdrfile_xtc.c:66:13: warning: unused variable ‘i’ [-Wunused-variable] 66 | int i,j,result; | ^ mdtraj/formats/xtc/src/xdrfile_xtc.c: In function ‘read_xtc_nframes’: mdtraj/formats/xtc/src/xdrfile_xtc.c:119:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 119 | if (NULL == xd) | ^~ mdtraj/formats/xtc/src/xdrfile_xtc.c:122:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 122 | do { | ^~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/xtc/xtc.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/xtc/xtc.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 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:719: /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:633:40: warning: ‘__pyx_v_status’ may be used uninitialized in this function [-Wmaybe-uninitialized] 633 | #define PyInt_FromLong PyLong_FromLong | ^~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:9474:7: note: ‘__pyx_v_status’ was declared here 9474 | int __pyx_v_status; | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c: In function ‘__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_12_read’: mdtraj/formats/xtc/xtc.c:7993:23: warning: ‘__pyx_pybuffernd_xyz_stride.diminfo[2].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 7993 | } else if (unlikely(__pyx_t_39 >= __pyx_pybuffernd_xyz_stride.diminfo[2].shape)) __pyx_t_6 = 2; | ^ mdtraj/formats/xtc/xtc.c:7989:23: warning: ‘__pyx_pybuffernd_xyz_stride.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 7989 | } else if (unlikely(__pyx_t_38 >= __pyx_pybuffernd_xyz_stride.diminfo[1].shape)) __pyx_t_6 = 1; | ^ mdtraj/formats/xtc/xtc.c:7985:23: warning: ‘__pyx_pybuffernd_xyz_stride.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 7985 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_xyz_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:7945:23: warning: ‘__pyx_pybuffernd_time_stride.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 7945 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_time_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:7927:23: warning: ‘__pyx_pybuffernd_step_stride.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 7927 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_step_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:8003:23: warning: ‘__pyx_pybuffernd_prec_stride.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 8003 | } else if (unlikely(__pyx_t_40 >= __pyx_pybuffernd_prec_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:7965:23: warning: ‘__pyx_pybuffernd_box_stride.diminfo[2].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 7965 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_box_stride.diminfo[2].shape)) __pyx_t_6 = 2; | ^ mdtraj/formats/xtc/xtc.c:7961:23: warning: ‘__pyx_pybuffernd_box_stride.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 7961 | } else if (unlikely(__pyx_t_33 >= __pyx_pybuffernd_box_stride.diminfo[1].shape)) __pyx_t_6 = 1; | ^ mdtraj/formats/xtc/xtc.c:7957:23: warning: ‘__pyx_pybuffernd_box_stride.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 7957 | } else if (unlikely(__pyx_t_32 >= __pyx_pybuffernd_box_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:7580:17: warning: ‘__pyx_pybuffernd_framebuffer.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 7580 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_framebuffer.diminfo[1].shape)) __pyx_t_6 = 1; | ^ mdtraj/formats/xtc/xtc.c:7576:17: warning: ‘__pyx_pybuffernd_framebuffer.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 7576 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_framebuffer.diminfo[0].shape)) __pyx_t_6 = 0; | ^ x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-x86_64-3.9/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-x86_64-3.9/mdtraj/formats/xtc/src/xdrfile_xtc.o build/temp.linux-x86_64-3.9/mdtraj/formats/xtc/xtc.o -o /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/xtc.cpython-39-x86_64-linux-gnu.so building 'mdtraj.formats.trr' extension x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/xtc/src/xdrfile.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_float’: mdtraj/formats/xtc/src/xdrfile.c:788:32: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 788 | int smallnum, smaller, larger, i, is_smaller, run; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c:785:23: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 785 | int smallidx, minidx, maxidx; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_float’: mdtraj/formats/xtc/src/xdrfile.c:1016:13: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable] 1016 | int errval=1; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_double’: mdtraj/formats/xtc/src/xdrfile.c:1305:32: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 1305 | int smallnum, smaller, larger, i, is_smaller, run; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c:1302:23: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 1302 | int smallidx, minidx, maxidx; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_double’: mdtraj/formats/xtc/src/xdrfile.c:1509:13: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable] 1509 | int errval=1; | ^~~~~~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/xtc/src/xdrfile_trr.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/xtc/src/xdrfile_trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/xtc/trr.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/xtc/trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 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:719: /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:633:40: warning: ‘__pyx_v_status’ may be used uninitialized in this function [-Wmaybe-uninitialized] 633 | #define PyInt_FromLong PyLong_FromLong | ^~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:11000:7: note: ‘__pyx_v_status’ was declared here 11000 | int __pyx_v_status; | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c: In function ‘__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_14_read’: mdtraj/formats/xtc/trr.c:8353:19: warning: ‘__pyx_pybuffernd_forces.diminfo[2].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 8353 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_forces.diminfo[2].shape)) __pyx_t_5 = 2; | ^ mdtraj/formats/xtc/trr.c:8349:19: warning: ‘__pyx_pybuffernd_forces.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 8349 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_forces.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:1864:90: warning: ‘__pyx_pybuffernd_forces.diminfo[0].strides’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1864 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) | ^ mdtraj/formats/xtc/trr.c:6890:21: note: ‘__pyx_pybuffernd_forces.diminfo[0].strides’ was declared here 6890 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8345:19: warning: ‘__pyx_pybuffernd_forces.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 8345 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_forces.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/trr.c:8296:19: warning: ‘__pyx_pybuffernd_vel.diminfo[2].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 8296 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_vel.diminfo[2].shape)) __pyx_t_5 = 2; | ^ mdtraj/formats/xtc/trr.c:8292:19: warning: ‘__pyx_pybuffernd_vel.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 8292 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_vel.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:1864:90: warning: ‘__pyx_pybuffernd_vel.diminfo[0].strides’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1864 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) | ^ mdtraj/formats/xtc/trr.c:6906:21: note: ‘__pyx_pybuffernd_vel.diminfo[0].strides’ was declared here 6906 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8288:19: warning: ‘__pyx_pybuffernd_vel.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 8288 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_vel.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/trr.c:8686:17: warning: ‘__pyx_pybuffernd_xyz_buffer.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 8686 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_xyz_buffer.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:8682:17: warning: ‘__pyx_pybuffernd_xyz_buffer.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 8682 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_xyz_buffer.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/trr.c:8527:19: warning: ‘__pyx_pybuffernd_vel_buffer.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 8527 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_vel_buffer.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:8523:19: warning: ‘__pyx_pybuffernd_vel_buffer.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 8523 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_vel_buffer.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/trr.c:8579:19: warning: ‘__pyx_pybuffernd_forces_buffer.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 8579 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_forces_buffer.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:8575:19: warning: ‘__pyx_pybuffernd_forces_buffer.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 8575 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_forces_buffer.diminfo[0].shape)) __pyx_t_5 = 0; | ^ x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-x86_64-3.9/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-x86_64-3.9/mdtraj/formats/xtc/src/xdrfile_trr.o build/temp.linux-x86_64-3.9/mdtraj/formats/xtc/trr.o -o /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/trr.cpython-39-x86_64-linux-gnu.so building 'mdtraj.formats.tng' extension creating build/temp.linux-x86_64-3.9/mdtraj/formats/tng creating build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src creating build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression creating build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/lib x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/bwlzh.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/bwlzh.o x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/bwt.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/bwt.o x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/coder.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/coder.o x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/dict.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/dict.o x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/fixpoint.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/fixpoint.o x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/huffman.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/huffman.o x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/huffmem.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/huffmem.o x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/lz77.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/lz77.o x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/merge_sort.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/merge_sort.o x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/mtf.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/mtf.o mdtraj/formats/tng/src/compression/mtf.c: In function ‘Ptngc_comp_conv_to_mtf’: mdtraj/formats/tng/src/compression/mtf.c:196:23: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 196 | while (dict[ptr]!=v) | ^~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/rle.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/rle.o mdtraj/formats/tng/src/compression/rle.c: In function ‘Ptngc_comp_conv_to_rle’: mdtraj/formats/tng/src/compression/rle.c:56:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 56 | if (v==vals[i]) | ^~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/tng_compress.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/tng_compress.o x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/vals16.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/vals16.o x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/warnmalloc.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/warnmalloc.o x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/widemuldiv.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/widemuldiv.o x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/xtc2.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/xtc2.o x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/xtc3.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/xtc3.o x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/lib/md5.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/lib/md5.o x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/lib/tng_io.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/lib/tng_io.o mdtraj/formats/tng/src/lib/tng_io.c: In function ‘tng_block_header_read’: mdtraj/formats/tng/src/lib/tng_io.c:1064:57: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int32_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint32_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, unsigned int *)’} [-Wincompatible-pointer-types] 1064 | tng_data->input_endianness_swap_func_32 = | ^ mdtraj/formats/tng/src/lib/tng_io.c:1073:57: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int64_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, long int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint64_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, long unsigned int *)’} [-Wincompatible-pointer-types] 1073 | tng_data->input_endianness_swap_func_64 = | ^ mdtraj/formats/tng/src/lib/tng_io.c:1089:57: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int32_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint32_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, unsigned int *)’} [-Wincompatible-pointer-types] 1089 | tng_data->input_endianness_swap_func_32 = | ^ mdtraj/formats/tng/src/lib/tng_io.c:1098:57: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int64_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, long int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint64_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, long unsigned int *)’} [-Wincompatible-pointer-types] 1098 | tng_data->input_endianness_swap_func_64 = | ^ mdtraj/formats/tng/src/lib/tng_io.c: In function ‘tng_output_file_endianness_get’: mdtraj/formats/tng/src/lib/tng_io.c:9565:53: warning: comparison of distinct pointer types lacks a cast 9565 | if(tng_data->output_endianness_swap_func_32 == | ^~ mdtraj/formats/tng/src/lib/tng_io.c:9570:58: warning: comparison of distinct pointer types lacks a cast 9570 | else if(tng_data->output_endianness_swap_func_32 == | ^~ mdtraj/formats/tng/src/lib/tng_io.c:9588:53: warning: comparison of distinct pointer types lacks a cast 9588 | if(tng_data->output_endianness_swap_func_64 == | ^~ mdtraj/formats/tng/src/lib/tng_io.c:9593:58: warning: comparison of distinct pointer types lacks a cast 9593 | else if(tng_data->output_endianness_swap_func_64 == | ^~ mdtraj/formats/tng/src/lib/tng_io.c: In function ‘tng_output_file_endianness_set’: mdtraj/formats/tng/src/lib/tng_io.c:9651:54: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int32_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint32_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, unsigned int *)’} [-Wincompatible-pointer-types] 9651 | tng_data->output_endianness_swap_func_32 = | ^ mdtraj/formats/tng/src/lib/tng_io.c:9660:54: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int64_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, long int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint64_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, long unsigned int *)’} [-Wincompatible-pointer-types] 9660 | tng_data->output_endianness_swap_func_64 = | ^ mdtraj/formats/tng/src/lib/tng_io.c:9673:54: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int32_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint32_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, unsigned int *)’} [-Wincompatible-pointer-types] 9673 | tng_data->output_endianness_swap_func_32 = | ^ mdtraj/formats/tng/src/lib/tng_io.c:9682:54: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int64_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, long int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint64_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, long unsigned int *)’} [-Wincompatible-pointer-types] 9682 | tng_data->output_endianness_swap_func_64 = | ^ In file included from /usr/include/string.h:519, from mdtraj/formats/tng/include/tng/tng_io.h:302, from mdtraj/formats/tng/src/lib/tng_io.c:20: In function ‘strncpy’, inlined from ‘tng_gen_data_block_add’ at mdtraj/formats/tng/src/lib/tng_io.c:12613:9: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:95:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-truncation] 95 | return __builtin___strncpy_chk (__dest, __src, __len, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 96 | __glibc_objsize (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/tng/src/lib/tng_io.c: In function ‘tng_gen_data_block_add’: mdtraj/formats/tng/src/lib/tng_io.c:12613:47: note: length computed here 12613 | strncpy(data->block_name, block_name, strlen(block_name) + 1); | ^~~~~~~~~~~~~~~~~~ mdtraj/formats/tng/src/lib/tng_io.c: In function ‘tng_data_block_write.isra’: mdtraj/formats/tng/src/lib/tng_io.c:5986:72: warning: ‘num_first_particle’ may be used uninitialized in this function [-Wmaybe-uninitialized] 5986 | for(j = num_first_particle; j < num_first_particle + n_particles; | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ mdtraj/formats/tng/src/lib/tng_io.c:4308:24: warning: ‘n_particles’ may be used uninitialized in this function [-Wmaybe-uninitialized] 4308 | dest = tng_compress_pos_float((float *)*data, (int)n_particles, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 4309 | (int)n_frames, | ~~~~~~~~~~~~~~ 4310 | f_precision, | ~~~~~~~~~~~~ 4311 | 0, alt_algo, | ~~~~~~~~~~~~ 4312 | &compressed_len); | ~~~~~~~~~~~~~~~~ mdtraj/formats/tng/src/lib/tng_io.c:5684:13: note: ‘n_particles’ was declared here 5684 | int64_t n_particles, num_first_particle, n_frames, stride_length; | ^~~~~~~~~~~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/tng.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/tng.o In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 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:745: /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:3627:104: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 3627 | __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:3682:88: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 3682 | __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:3714:90: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 3714 | __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:3746:95: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 3746 | __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:3816:113: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 3816 | __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:3860:77: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 3860 | __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:4656:106: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 4656 | __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:4701:108: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 4701 | __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:4808:115: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 4808 | __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:4838:105: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 4838 | __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:4966:105: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 4966 | __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:5567:126: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 5567 | __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:5977:152: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 5977 | __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:6245:108: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 6245 | __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:6347:304: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 6347 | __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:8839:94: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 8839 | __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:8871:75: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 8871 | __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:8903:81: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 8903 | __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:9226:77: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 9226 | __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:9417:372: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 9417 | __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:9469:378: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 9469 | __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:9531:89: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 9531 | __pyx_t_1 = ((tng_frame_set_first_frame_time_set(__pyx_v_self->_traj, __pyx_t_15) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/bwlzh.o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/bwt.o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/coder.o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/dict.o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/fixpoint.o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/huffman.o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/huffmem.o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/lz77.o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/merge_sort.o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/mtf.o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/rle.o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/tng_compress.o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/vals16.o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/warnmalloc.o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/widemuldiv.o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/xtc2.o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/xtc3.o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/lib/md5.o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/lib/tng_io.o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/tng.o -lz -o /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/tng.cpython-39-x86_64-linux-gnu.so building 'mdtraj.formats.dcd' extension creating build/temp.linux-x86_64-3.9/mdtraj/formats/dcd creating build/temp.linux-x86_64-3.9/mdtraj/formats/dcd/src x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/dcd/include/ -Imdtraj/formats/dcd/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/dcd/dcd.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/dcd/dcd.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 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:717: /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:631:40: warning: ‘__pyx_v_i’ may be used uninitialized in this function [-Wmaybe-uninitialized] 631 | #define PyInt_FromLong PyLong_FromLong | ^~~~~~~~~~~~~~~ mdtraj/formats/dcd/dcd.c:5369:7: note: ‘__pyx_v_i’ was declared here 5369 | int __pyx_v_i; | ^~~~~~~~~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/dcd/include/ -Imdtraj/formats/dcd/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/dcd/src/dcdplugin.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/dcd/src/dcdplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/mdtraj/formats/dcd/dcd.o build/temp.linux-x86_64-3.9/mdtraj/formats/dcd/src/dcdplugin.o -o /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/dcd.cpython-39-x86_64-linux-gnu.so building 'mdtraj.formats.binpos' extension creating build/temp.linux-x86_64-3.9/mdtraj/formats/binpos creating build/temp.linux-x86_64-3.9/mdtraj/formats/binpos/src x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/binpos/include/ -Imdtraj/formats/binpos/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/binpos/binpos.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/binpos/binpos.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 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:717: /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:5447:6: warning: ‘__pyx_v_status’ may be used uninitialized [-Wmaybe-uninitialized] 5447 | if (__pyx_t_2) { | ^ mdtraj/formats/binpos/binpos.c:4927:7: note: ‘__pyx_v_status’ was declared here 4927 | int __pyx_v_status; | ^~~~~~~~~~~~~~ mdtraj/formats/binpos/binpos.c:631:40: warning: ‘__pyx_v_i’ may be used uninitialized in this function [-Wmaybe-uninitialized] 631 | #define PyInt_FromLong PyLong_FromLong | ^~~~~~~~~~~~~~~ mdtraj/formats/binpos/binpos.c:4924:7: note: ‘__pyx_v_i’ was declared here 4924 | int __pyx_v_i; | ^~~~~~~~~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/binpos/include/ -Imdtraj/formats/binpos/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/binpos/src/binposplugin.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/binpos/src/binposplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/mdtraj/formats/binpos/binpos.o build/temp.linux-x86_64-3.9/mdtraj/formats/binpos/src/binposplugin.o -o /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/binpos.cpython-39-x86_64-linux-gnu.so building 'mdtraj.formats.dtr' extension creating build/temp.linux-x86_64-3.9/mdtraj/formats/dtr creating build/temp.linux-x86_64-3.9/mdtraj/formats/dtr/src x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/dtr/dtr.cpp -o build/temp.linux-x86_64-3.9/mdtraj/formats/dtr/dtr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 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:738: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/dtr/src/dtrplugin.cxx -o build/temp.linux-x86_64-3.9/mdtraj/formats/dtr/src/dtrplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/formats/dtr/src/dtrplugin.cxx: In member function ‘bool desres::molfile::Timekeys::init(const string&)’: mdtraj/formats/dtr/src/dtrplugin.cxx:487:27: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 487 | printf("size %d framesize %d\n\n", | ~^ | | | int | %ld 488 | keys[i].size(), m_framesize); | ~~~~~~~~~~~~~~ | | | uint64_t {aka long unsigned int} mdtraj/formats/dtr/src/dtrplugin.cxx:487:40: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 487 | printf("size %d framesize %d\n\n", | ~^ | | | int | %ld 488 | keys[i].size(), m_framesize); | ~~~~~~~~~~~ | | | uint64_t {aka long unsigned int} mdtraj/formats/dtr/src/dtrplugin.cxx: In constructor ‘{anonymous}::DDException::DDException(const string&, int)’: mdtraj/formats/dtr/src/dtrplugin.cxx:680:43: warning: ‘*this.{anonymous}::DDException::eno’ is used uninitialized [-Wuninitialized] 680 | : std::runtime_error(text + strerror(eno)), eno(_eno){} | ~~~~~~~~^~~~~ mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘void DDmkdir(const string&, mode_t, int, int)’: mdtraj/formats/dtr/src/dtrplugin.cxx:706:23: warning: ‘%03x’ directive writing between 3 and 8 bytes into a region of size 6 [-Wformat-overflow=] 706 | sprintf(sub, "%03x/", i); | ^~~~ mdtraj/formats/dtr/src/dtrplugin.cxx:706:22: note: directive argument in the range [0, 2147483646] 706 | sprintf(sub, "%03x/", i); | ^~~~~~~ In file included from /usr/include/stdio.h:866, from mdtraj/formats/dtr/include/molfile_plugin.h:35, from mdtraj/formats/dtr/include/dtrplugin.hxx:46, from mdtraj/formats/dtr/src/dtrplugin.cxx:42: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 5 and 10 bytes into a destination of size 6 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 40 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ mdtraj/formats/dtr/src/dtrplugin.cxx:714:30: warning: ‘%03x’ directive writing between 3 and 8 bytes into a region of size 6 [-Wformat-overflow=] 714 | sprintf(subsub, "%03x", j); | ^~~~ mdtraj/formats/dtr/src/dtrplugin.cxx:714:29: note: directive argument in the range [0, 2147483646] 714 | sprintf(subsub, "%03x", j); | ^~~~~~ In file included from /usr/include/stdio.h:866, from mdtraj/formats/dtr/include/molfile_plugin.h:35, from mdtraj/formats/dtr/include/dtrplugin.hxx:46, from mdtraj/formats/dtr/src/dtrplugin.cxx:42: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 4 and 9 bytes into a destination of size 6 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 40 | __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:667:35: 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:866, from mdtraj/formats/dtr/include/molfile_plugin.h:35, from mdtraj/formats/dtr/include/dtrplugin.hxx:46, from mdtraj/formats/dtr/src/dtrplugin.cxx:42: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 5 and 10 bytes into a destination of size 9 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 40 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ mdtraj/formats/dtr/src/dtrplugin.cxx:665:35: warning: ‘%03x’ directive writing between 3 and 8 bytes into a region of size between 0 and 5 [-Wformat-overflow=] 665 | sprintf(answer, "%03x/%03x/", d1, d2); | ^~~~ mdtraj/formats/dtr/src/dtrplugin.cxx:665:29: note: directive argument in the range [0, 2147483646] 665 | sprintf(answer, "%03x/%03x/", d1, d2); | ^~~~~~~~~~~~ In file included from /usr/include/stdio.h:866, from mdtraj/formats/dtr/include/molfile_plugin.h:35, from mdtraj/formats/dtr/include/dtrplugin.hxx:46, from mdtraj/formats/dtr/src/dtrplugin.cxx:42: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 9 and 19 bytes into a destination of size 9 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 40 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/mdtraj/formats/dtr/dtr.o build/temp.linux-x86_64-3.9/mdtraj/formats/dtr/src/dtrplugin.o -o /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/dtr.cpython-39-x86_64-linux-gnu.so building 'mdtraj._rmsd' extension creating build/temp.linux-x86_64-3.9/mdtraj/rmsd creating build/temp.linux-x86_64-3.9/mdtraj/rmsd/src x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/_rmsd.cpp -o build/temp.linux-x86_64-3.9/mdtraj/rmsd/_rmsd.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-x86_64-3.9/mdtraj/rmsd/src/center.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/src/rotation.cpp -o build/temp.linux-x86_64-3.9/mdtraj/rmsd/src/rotation.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-x86_64-3.9/mdtraj/rmsd/src/theobald_rmsd.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/mdtraj/rmsd/_rmsd.o build/temp.linux-x86_64-3.9/mdtraj/rmsd/src/center.o build/temp.linux-x86_64-3.9/mdtraj/rmsd/src/rotation.o build/temp.linux-x86_64-3.9/mdtraj/rmsd/src/theobald_rmsd.o -lgomp -o /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/_rmsd.cpython-39-x86_64-linux-gnu.so building 'mdtraj._lprmsd' extension x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/_lprmsd.cpp -o build/temp.linux-x86_64-3.9/mdtraj/rmsd/_lprmsd.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 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:749: /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 ‘PyObject* __pyx_pf_6mdtraj_7_lprmsd_lprmsd(PyObject*, PyObject*, PyObject*, int, PyObject*, PyObject*, PyLongObject*, PyLongObject*)’: mdtraj/rmsd/_lprmsd.cpp:4021:14: 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] 4021 | } else if (unlikely(__pyx_t_34 >= __pyx_pybuffernd_ref_xyz_frame_dis.diminfo[0].shape)) __pyx_t_33 = 0; | ^~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/src/Munkres.cpp -o build/temp.linux-x86_64-3.9/mdtraj/rmsd/src/Munkres.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-x86_64-3.9/mdtraj/rmsd/src/center.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/src/euclidean_permutation.cpp -o build/temp.linux-x86_64-3.9/mdtraj/rmsd/src/euclidean_permutation.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/src/fancy_index.cpp -o build/temp.linux-x86_64-3.9/mdtraj/rmsd/src/fancy_index.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/src/rotation.cpp -o build/temp.linux-x86_64-3.9/mdtraj/rmsd/src/rotation.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-x86_64-3.9/mdtraj/rmsd/src/theobald_rmsd.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/mdtraj/rmsd/_lprmsd.o build/temp.linux-x86_64-3.9/mdtraj/rmsd/src/Munkres.o build/temp.linux-x86_64-3.9/mdtraj/rmsd/src/center.o build/temp.linux-x86_64-3.9/mdtraj/rmsd/src/euclidean_permutation.o build/temp.linux-x86_64-3.9/mdtraj/rmsd/src/fancy_index.o build/temp.linux-x86_64-3.9/mdtraj/rmsd/src/rotation.o build/temp.linux-x86_64-3.9/mdtraj/rmsd/src/theobald_rmsd.o -lgomp -o /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/_lprmsd.cpython-39-x86_64-linux-gnu.so building 'mdtraj.core.lib.libtheobald' extension x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-x86_64-3.9/mdtraj/rmsd/src/theobald_rmsd.o -msse2 -mssse3 -O3 -funroll-loops --std=c++11 x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-x86_64-3.9/mdtraj/rmsd/src/center.o -msse2 -mssse3 -O3 -funroll-loops --std=c++11 x86_64-linux-gnu-gcc-ar rcs /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/core/lib/libtheobald.a build/temp.linux-x86_64-3.9/mdtraj/rmsd/src/theobald_rmsd.o build/temp.linux-x86_64-3.9/mdtraj/rmsd/src/center.o building 'mdtraj.geometry._geometry' extension creating build/temp.linux-x86_64-3.9/mdtraj/geometry creating build/temp.linux-x86_64-3.9/mdtraj/geometry/src x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/geometry/src/_geometry.cpp -o build/temp.linux-x86_64-3.9/mdtraj/geometry/src/_geometry.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 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:751: /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:6022:224: warning: ‘__pyx_v_delta[2]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 6022 | (__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:6036:277: warning: ‘__pyx_v_delta[1]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 6036 | (__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:6036:277: warning: ‘__pyx_v_offset[1]’ may be used uninitialized in this function [-Wmaybe-uninitialized] x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/geometry/src/dssp.cpp -o build/temp.linux-x86_64-3.9/mdtraj/geometry/src/dssp.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/geometry/src/geometry.cpp -o build/temp.linux-x86_64-3.9/mdtraj/geometry/src/geometry.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/geometry/src/sasa.cpp -o build/temp.linux-x86_64-3.9/mdtraj/geometry/src/sasa.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/mdtraj/geometry/src/_geometry.o build/temp.linux-x86_64-3.9/mdtraj/geometry/src/dssp.o build/temp.linux-x86_64-3.9/mdtraj/geometry/src/geometry.o build/temp.linux-x86_64-3.9/mdtraj/geometry/src/sasa.o -lgomp -o /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/_geometry.cpython-39-x86_64-linux-gnu.so building 'mdtraj.geometry.drid' extension x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/geometry/drid.cpp -o build/temp.linux-x86_64-3.9/mdtraj/geometry/drid.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/geometry/src/dridkernels.cpp -o build/temp.linux-x86_64-3.9/mdtraj/geometry/src/dridkernels.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/geometry/src/moments.cpp -o build/temp.linux-x86_64-3.9/mdtraj/geometry/src/moments.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/mdtraj/geometry/drid.o build/temp.linux-x86_64-3.9/mdtraj/geometry/src/dridkernels.o build/temp.linux-x86_64-3.9/mdtraj/geometry/src/moments.o -lgomp -o /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/drid.cpython-39-x86_64-linux-gnu.so building 'mdtraj.geometry.neighbors' extension x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/geometry/neighbors.cpp -o build/temp.linux-x86_64-3.9/mdtraj/geometry/neighbors.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/geometry/src/neighbors.cpp -o build/temp.linux-x86_64-3.9/mdtraj/geometry/src/neighbors.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/mdtraj/geometry/neighbors.o build/temp.linux-x86_64-3.9/mdtraj/geometry/src/neighbors.o -lgomp -o /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/neighbors.cpython-39-x86_64-linux-gnu.so building 'mdtraj.geometry.neighborlist' extension x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/geometry/neighborlist.cpp -o build/temp.linux-x86_64-3.9/mdtraj/geometry/neighborlist.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/geometry/src/neighborlist.cpp -o build/temp.linux-x86_64-3.9/mdtraj/geometry/src/neighborlist.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In constructor ‘Voxels::Voxels(float, float, float, float, float, float, const float (&)[3][3], bool)’, inlined from ‘std::vector > _compute_neighborlist(const float*, int, float, const float*)’ at mdtraj/geometry/src/neighborlist.cpp:377:116: mdtraj/geometry/src/neighborlist.cpp:50:53: warning: ‘periodicBoxVectors’ may be used uninitialized [-Wmaybe-uninitialized] 50 | periodicBoxSize[0] = periodicBoxVectors[0][0]; | ~~~~~~~~~~~~~~~~~~~~~~~^ mdtraj/geometry/src/neighborlist.cpp: In function ‘std::vector > _compute_neighborlist(const float*, int, float, const float*)’: mdtraj/geometry/src/neighborlist.cpp:341:11: note: ‘periodicBoxVectors’ declared here 341 | float periodicBoxVectors[3][3]; | ^~~~~~~~~~~~~~~~~~ In constructor ‘Voxels::Voxels(float, float, float, float, float, float, const float (&)[3][3], bool)’, inlined from ‘std::vector > _compute_neighborlist(const float*, int, float, const float*)’ at mdtraj/geometry/src/neighborlist.cpp:377:116: mdtraj/geometry/src/neighborlist.cpp:56:45: warning: ‘periodicBoxVectors’ may be used uninitialized [-Wmaybe-uninitialized] 56 | triclinic = (periodicBoxVectors[0][1] != 0.0 || periodicBoxVectors[0][2] != 0.0 || | ~~~~~~~~~~~~~~~~~~~~~~~^ mdtraj/geometry/src/neighborlist.cpp: In function ‘std::vector > _compute_neighborlist(const float*, int, float, const float*)’: mdtraj/geometry/src/neighborlist.cpp:341:11: note: ‘periodicBoxVectors’ declared here 341 | float periodicBoxVectors[3][3]; | ^~~~~~~~~~~~~~~~~~ mdtraj/geometry/src/neighborlist.cpp:374:49: warning: ‘periodicBoxVectors’ may be used uninitialized [-Wmaybe-uninitialized] 374 | edgeSizeY = 0.6f*periodicBoxVectors[1][1]/floorf(periodicBoxVectors[1][1]/maxDistance); | ~~~~~~~~~~~~~~~~~~~~~~~^ mdtraj/geometry/src/neighborlist.cpp:341:11: note: ‘periodicBoxVectors’ declared here 341 | float periodicBoxVectors[3][3]; | ^~~~~~~~~~~~~~~~~~ mdtraj/geometry/src/neighborlist.cpp:375:49: warning: ‘periodicBoxVectors’ may be used uninitialized [-Wmaybe-uninitialized] 375 | edgeSizeZ = 0.6f*periodicBoxVectors[2][2]/floorf(periodicBoxVectors[2][2]/maxDistance); | ~~~~~~~~~~~~~~~~~~~~~~~^ mdtraj/geometry/src/neighborlist.cpp:341:11: note: ‘periodicBoxVectors’ declared here 341 | float periodicBoxVectors[3][3]; | ^~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/mdtraj/geometry/neighborlist.o build/temp.linux-x86_64-3.9/mdtraj/geometry/src/neighborlist.o -lgomp -o /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/neighborlist.cpython-39-x86_64-linux-gnu.so I: pybuild base:237: /usr/bin/python3 setup.py build Using built-in specs. COLLECT_GCC=/usr/bin/x86_64-linux-gnu-gcc COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/11/lto-wrapper OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa OFFLOAD_TARGET_DEFAULT=1 Target: x86_64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 11.2.0-19' --with-bugurl=file:///usr/share/doc/gcc-11/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-11 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --enable-cet --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/gcc-11-uiwEqG/gcc-11-11.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-11-uiwEqG/gcc-11-11.2.0/debian/tmp-gcn/usr --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=2 Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 11.2.0 (Debian 11.2.0-19) 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/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj copying mdtraj/__init__.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj copying mdtraj/io.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj copying mdtraj/version.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj creating /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/core copying mdtraj/core/__init__.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/core copying mdtraj/core/element.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/core copying mdtraj/core/residue_names.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/core copying mdtraj/core/selection.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/core copying mdtraj/core/topology.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/core copying mdtraj/core/trajectory.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/core creating /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/formats copying mdtraj/formats/__init__.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/formats copying mdtraj/formats/amberrst.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/formats copying mdtraj/formats/arc.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/formats copying mdtraj/formats/gro.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/formats copying mdtraj/formats/gsd.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/formats copying mdtraj/formats/hdf5.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/formats copying mdtraj/formats/hoomdxml.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/formats copying mdtraj/formats/lammpstrj.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/formats copying mdtraj/formats/lh5.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/formats copying mdtraj/formats/mdcrd.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/formats copying mdtraj/formats/mol2.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/formats copying mdtraj/formats/netcdf.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/formats copying mdtraj/formats/openmmxml.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/formats copying mdtraj/formats/prmtop.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/formats copying mdtraj/formats/psf.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/formats copying mdtraj/formats/registry.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/formats copying mdtraj/formats/xyzfile.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/formats creating /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/__init__.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/alignment.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/angle.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/contact.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/dihedral.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/distance.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/dssp.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/hbond.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/internal.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/order.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/rdf.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/rg.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/sasa.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/shape.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/thermodynamic_properties.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/geometry creating /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/nmr copying mdtraj/nmr/__init__.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/nmr copying mdtraj/nmr/scalar_couplings.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/nmr copying mdtraj/nmr/shift_wrappers.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/nmr creating /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/__init__.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/basereporter.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/dcdreporter.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/hdf5reporter.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/netcdfreporter.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/xtcreporter.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/reporters creating /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/scripts copying mdtraj/scripts/__init__.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/scripts copying mdtraj/scripts/mdconvert.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/scripts copying mdtraj/scripts/mdinspect.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/scripts creating /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/testing copying mdtraj/testing/__init__.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/testing copying mdtraj/testing/docscrape.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/testing copying mdtraj/testing/docstrings.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/testing copying mdtraj/testing/testing.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/testing creating /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/utils copying mdtraj/utils/__init__.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/utils copying mdtraj/utils/contextmanagers.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/utils copying mdtraj/utils/delay_import.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/utils copying mdtraj/utils/rotation.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/utils copying mdtraj/utils/singleton.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/utils copying mdtraj/utils/six.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/utils copying mdtraj/utils/unitcell.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/utils copying mdtraj/utils/validation.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/utils copying mdtraj/utils/zipped.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/utils creating /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/formats/pdb copying mdtraj/formats/pdb/__init__.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/formats/pdb copying mdtraj/formats/pdb/pdbfile.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/formats/pdb copying mdtraj/formats/pdb/pdbstructure.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/formats/pdb creating /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/__init__.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/basedimension.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/baseunit.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/doctests.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/mymatrix.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/unit.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/constants.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/prefix.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/quantity.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/standard_dimensions.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/unit_definitions.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/unit_math.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/unit_operators.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/utils/unit creating /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/formats/pdb/data copying mdtraj/formats/pdb/data/pdbNames.xml -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/formats/pdb/data copying mdtraj/formats/pdb/data/residues.xml -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/formats/pdb/data running build_ext building 'mdtraj.formats.xtc' extension creating build/temp.linux-x86_64-3.10 creating build/temp.linux-x86_64-3.10/mdtraj creating build/temp.linux-x86_64-3.10/mdtraj/formats creating build/temp.linux-x86_64-3.10/mdtraj/formats/xtc creating build/temp.linux-x86_64-3.10/mdtraj/formats/xtc/src x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -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/python3.10 -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.linux-x86_64-3.10/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -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/python3.10 -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-x86_64-3.10/mdtraj/formats/xtc/src/xdrfile.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_float’: mdtraj/formats/xtc/src/xdrfile.c:788:32: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 788 | int smallnum, smaller, larger, i, is_smaller, run; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c:785:23: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 785 | int smallidx, minidx, maxidx; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_float’: mdtraj/formats/xtc/src/xdrfile.c:1016:13: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable] 1016 | int errval=1; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_double’: mdtraj/formats/xtc/src/xdrfile.c:1305:32: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 1305 | int smallnum, smaller, larger, i, is_smaller, run; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c:1302:23: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 1302 | int smallidx, minidx, maxidx; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_double’: mdtraj/formats/xtc/src/xdrfile.c:1509:13: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable] 1509 | int errval=1; | ^~~~~~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -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/python3.10 -c mdtraj/formats/xtc/src/xdrfile_xtc.c -o build/temp.linux-x86_64-3.10/mdtraj/formats/xtc/src/xdrfile_xtc.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/formats/xtc/src/xdrfile_xtc.c: In function ‘xtc_coord’: mdtraj/formats/xtc/src/xdrfile_xtc.c:66:15: warning: unused variable ‘j’ [-Wunused-variable] 66 | int i,j,result; | ^ mdtraj/formats/xtc/src/xdrfile_xtc.c:66:13: warning: unused variable ‘i’ [-Wunused-variable] 66 | int i,j,result; | ^ mdtraj/formats/xtc/src/xdrfile_xtc.c: In function ‘read_xtc_nframes’: mdtraj/formats/xtc/src/xdrfile_xtc.c:119:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 119 | if (NULL == xd) | ^~ mdtraj/formats/xtc/src/xdrfile_xtc.c:122:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 122 | do { | ^~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -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/python3.10 -c mdtraj/formats/xtc/xtc.c -o build/temp.linux-x86_64-3.10/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:1969, 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:719: /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:633:40: warning: ‘__pyx_v_status’ may be used uninitialized in this function [-Wmaybe-uninitialized] 633 | #define PyInt_FromLong PyLong_FromLong | ^~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:9474:7: note: ‘__pyx_v_status’ was declared here 9474 | int __pyx_v_status; | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c: In function ‘__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_12_read’: mdtraj/formats/xtc/xtc.c:7993:23: warning: ‘__pyx_pybuffernd_xyz_stride.diminfo[2].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 7993 | } else if (unlikely(__pyx_t_39 >= __pyx_pybuffernd_xyz_stride.diminfo[2].shape)) __pyx_t_6 = 2; | ^ mdtraj/formats/xtc/xtc.c:7989:23: warning: ‘__pyx_pybuffernd_xyz_stride.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 7989 | } else if (unlikely(__pyx_t_38 >= __pyx_pybuffernd_xyz_stride.diminfo[1].shape)) __pyx_t_6 = 1; | ^ mdtraj/formats/xtc/xtc.c:7985:23: warning: ‘__pyx_pybuffernd_xyz_stride.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 7985 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_xyz_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:7945:23: warning: ‘__pyx_pybuffernd_time_stride.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 7945 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_time_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:7927:23: warning: ‘__pyx_pybuffernd_step_stride.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 7927 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_step_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:8003:23: warning: ‘__pyx_pybuffernd_prec_stride.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 8003 | } else if (unlikely(__pyx_t_40 >= __pyx_pybuffernd_prec_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:7965:23: warning: ‘__pyx_pybuffernd_box_stride.diminfo[2].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 7965 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_box_stride.diminfo[2].shape)) __pyx_t_6 = 2; | ^ mdtraj/formats/xtc/xtc.c:7961:23: warning: ‘__pyx_pybuffernd_box_stride.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 7961 | } else if (unlikely(__pyx_t_33 >= __pyx_pybuffernd_box_stride.diminfo[1].shape)) __pyx_t_6 = 1; | ^ mdtraj/formats/xtc/xtc.c:7957:23: warning: ‘__pyx_pybuffernd_box_stride.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 7957 | } else if (unlikely(__pyx_t_32 >= __pyx_pybuffernd_box_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:7580:17: warning: ‘__pyx_pybuffernd_framebuffer.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 7580 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_framebuffer.diminfo[1].shape)) __pyx_t_6 = 1; | ^ mdtraj/formats/xtc/xtc.c:7576:17: warning: ‘__pyx_pybuffernd_framebuffer.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 7576 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_framebuffer.diminfo[0].shape)) __pyx_t_6 = 0; | ^ x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.10/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-x86_64-3.10/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-x86_64-3.10/mdtraj/formats/xtc/src/xdrfile_xtc.o build/temp.linux-x86_64-3.10/mdtraj/formats/xtc/xtc.o -o /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/formats/xtc.cpython-310-x86_64-linux-gnu.so building 'mdtraj.formats.trr' extension x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -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/python3.10 -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.linux-x86_64-3.10/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -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/python3.10 -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-x86_64-3.10/mdtraj/formats/xtc/src/xdrfile.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_float’: mdtraj/formats/xtc/src/xdrfile.c:788:32: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 788 | int smallnum, smaller, larger, i, is_smaller, run; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c:785:23: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 785 | int smallidx, minidx, maxidx; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_float’: mdtraj/formats/xtc/src/xdrfile.c:1016:13: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable] 1016 | int errval=1; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_double’: mdtraj/formats/xtc/src/xdrfile.c:1305:32: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 1305 | int smallnum, smaller, larger, i, is_smaller, run; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c:1302:23: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 1302 | int smallidx, minidx, maxidx; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_double’: mdtraj/formats/xtc/src/xdrfile.c:1509:13: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable] 1509 | int errval=1; | ^~~~~~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -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/python3.10 -c mdtraj/formats/xtc/src/xdrfile_trr.c -o build/temp.linux-x86_64-3.10/mdtraj/formats/xtc/src/xdrfile_trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -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/python3.10 -c mdtraj/formats/xtc/trr.c -o build/temp.linux-x86_64-3.10/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:1969, 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:719: /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:633:40: warning: ‘__pyx_v_status’ may be used uninitialized in this function [-Wmaybe-uninitialized] 633 | #define PyInt_FromLong PyLong_FromLong | ^~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:11000:7: note: ‘__pyx_v_status’ was declared here 11000 | int __pyx_v_status; | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c: In function ‘__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_14_read’: mdtraj/formats/xtc/trr.c:8353:19: warning: ‘__pyx_pybuffernd_forces.diminfo[2].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 8353 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_forces.diminfo[2].shape)) __pyx_t_5 = 2; | ^ mdtraj/formats/xtc/trr.c:8349:19: warning: ‘__pyx_pybuffernd_forces.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 8349 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_forces.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:1864:90: warning: ‘__pyx_pybuffernd_forces.diminfo[0].strides’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1864 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) | ^ mdtraj/formats/xtc/trr.c:6890:21: note: ‘__pyx_pybuffernd_forces.diminfo[0].strides’ was declared here 6890 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8345:19: warning: ‘__pyx_pybuffernd_forces.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 8345 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_forces.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/trr.c:8296:19: warning: ‘__pyx_pybuffernd_vel.diminfo[2].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 8296 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_vel.diminfo[2].shape)) __pyx_t_5 = 2; | ^ mdtraj/formats/xtc/trr.c:8292:19: warning: ‘__pyx_pybuffernd_vel.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 8292 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_vel.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:1864:90: warning: ‘__pyx_pybuffernd_vel.diminfo[0].strides’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1864 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) | ^ mdtraj/formats/xtc/trr.c:6906:21: note: ‘__pyx_pybuffernd_vel.diminfo[0].strides’ was declared here 6906 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8288:19: warning: ‘__pyx_pybuffernd_vel.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 8288 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_vel.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/trr.c:8686:17: warning: ‘__pyx_pybuffernd_xyz_buffer.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 8686 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_xyz_buffer.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:8682:17: warning: ‘__pyx_pybuffernd_xyz_buffer.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 8682 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_xyz_buffer.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/trr.c:8527:19: warning: ‘__pyx_pybuffernd_vel_buffer.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 8527 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_vel_buffer.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:8523:19: warning: ‘__pyx_pybuffernd_vel_buffer.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 8523 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_vel_buffer.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/trr.c:8579:19: warning: ‘__pyx_pybuffernd_forces_buffer.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 8579 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_forces_buffer.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:8575:19: warning: ‘__pyx_pybuffernd_forces_buffer.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 8575 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_forces_buffer.diminfo[0].shape)) __pyx_t_5 = 0; | ^ x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.10/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-x86_64-3.10/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-x86_64-3.10/mdtraj/formats/xtc/src/xdrfile_trr.o build/temp.linux-x86_64-3.10/mdtraj/formats/xtc/trr.o -o /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/formats/trr.cpython-310-x86_64-linux-gnu.so building 'mdtraj.formats.tng' extension creating build/temp.linux-x86_64-3.10/mdtraj/formats/tng creating build/temp.linux-x86_64-3.10/mdtraj/formats/tng/src creating build/temp.linux-x86_64-3.10/mdtraj/formats/tng/src/compression creating build/temp.linux-x86_64-3.10/mdtraj/formats/tng/src/lib x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -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/python3.10 -c mdtraj/formats/tng/src/compression/bwlzh.c -o build/temp.linux-x86_64-3.10/mdtraj/formats/tng/src/compression/bwlzh.o x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -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/python3.10 -c mdtraj/formats/tng/src/compression/bwt.c -o build/temp.linux-x86_64-3.10/mdtraj/formats/tng/src/compression/bwt.o x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -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/python3.10 -c mdtraj/formats/tng/src/compression/coder.c -o build/temp.linux-x86_64-3.10/mdtraj/formats/tng/src/compression/coder.o x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -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/python3.10 -c mdtraj/formats/tng/src/compression/dict.c -o build/temp.linux-x86_64-3.10/mdtraj/formats/tng/src/compression/dict.o x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -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/python3.10 -c mdtraj/formats/tng/src/compression/fixpoint.c -o build/temp.linux-x86_64-3.10/mdtraj/formats/tng/src/compression/fixpoint.o x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -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/python3.10 -c mdtraj/formats/tng/src/compression/huffman.c -o build/temp.linux-x86_64-3.10/mdtraj/formats/tng/src/compression/huffman.o x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -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/python3.10 -c mdtraj/formats/tng/src/compression/huffmem.c -o build/temp.linux-x86_64-3.10/mdtraj/formats/tng/src/compression/huffmem.o x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -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/python3.10 -c mdtraj/formats/tng/src/compression/lz77.c -o build/temp.linux-x86_64-3.10/mdtraj/formats/tng/src/compression/lz77.o x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -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/python3.10 -c mdtraj/formats/tng/src/compression/merge_sort.c -o build/temp.linux-x86_64-3.10/mdtraj/formats/tng/src/compression/merge_sort.o x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -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/python3.10 -c mdtraj/formats/tng/src/compression/mtf.c -o build/temp.linux-x86_64-3.10/mdtraj/formats/tng/src/compression/mtf.o mdtraj/formats/tng/src/compression/mtf.c: In function ‘Ptngc_comp_conv_to_mtf’: mdtraj/formats/tng/src/compression/mtf.c:196:23: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 196 | while (dict[ptr]!=v) | ^~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -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/python3.10 -c mdtraj/formats/tng/src/compression/rle.c -o build/temp.linux-x86_64-3.10/mdtraj/formats/tng/src/compression/rle.o mdtraj/formats/tng/src/compression/rle.c: In function ‘Ptngc_comp_conv_to_rle’: mdtraj/formats/tng/src/compression/rle.c:56:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 56 | if (v==vals[i]) | ^~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -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/python3.10 -c mdtraj/formats/tng/src/compression/tng_compress.c -o build/temp.linux-x86_64-3.10/mdtraj/formats/tng/src/compression/tng_compress.o x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -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/python3.10 -c mdtraj/formats/tng/src/compression/vals16.c -o build/temp.linux-x86_64-3.10/mdtraj/formats/tng/src/compression/vals16.o x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -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/python3.10 -c mdtraj/formats/tng/src/compression/warnmalloc.c -o build/temp.linux-x86_64-3.10/mdtraj/formats/tng/src/compression/warnmalloc.o x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -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/python3.10 -c mdtraj/formats/tng/src/compression/widemuldiv.c -o build/temp.linux-x86_64-3.10/mdtraj/formats/tng/src/compression/widemuldiv.o x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -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/python3.10 -c mdtraj/formats/tng/src/compression/xtc2.c -o build/temp.linux-x86_64-3.10/mdtraj/formats/tng/src/compression/xtc2.o x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -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/python3.10 -c mdtraj/formats/tng/src/compression/xtc3.c -o build/temp.linux-x86_64-3.10/mdtraj/formats/tng/src/compression/xtc3.o x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -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/python3.10 -c mdtraj/formats/tng/src/lib/md5.c -o build/temp.linux-x86_64-3.10/mdtraj/formats/tng/src/lib/md5.o x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -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/python3.10 -c mdtraj/formats/tng/src/lib/tng_io.c -o build/temp.linux-x86_64-3.10/mdtraj/formats/tng/src/lib/tng_io.o mdtraj/formats/tng/src/lib/tng_io.c: In function ‘tng_block_header_read’: mdtraj/formats/tng/src/lib/tng_io.c:1064:57: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int32_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint32_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, unsigned int *)’} [-Wincompatible-pointer-types] 1064 | tng_data->input_endianness_swap_func_32 = | ^ mdtraj/formats/tng/src/lib/tng_io.c:1073:57: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int64_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, long int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint64_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, long unsigned int *)’} [-Wincompatible-pointer-types] 1073 | tng_data->input_endianness_swap_func_64 = | ^ mdtraj/formats/tng/src/lib/tng_io.c:1089:57: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int32_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint32_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, unsigned int *)’} [-Wincompatible-pointer-types] 1089 | tng_data->input_endianness_swap_func_32 = | ^ mdtraj/formats/tng/src/lib/tng_io.c:1098:57: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int64_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, long int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint64_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, long unsigned int *)’} [-Wincompatible-pointer-types] 1098 | tng_data->input_endianness_swap_func_64 = | ^ mdtraj/formats/tng/src/lib/tng_io.c: In function ‘tng_output_file_endianness_get’: mdtraj/formats/tng/src/lib/tng_io.c:9565:53: warning: comparison of distinct pointer types lacks a cast 9565 | if(tng_data->output_endianness_swap_func_32 == | ^~ mdtraj/formats/tng/src/lib/tng_io.c:9570:58: warning: comparison of distinct pointer types lacks a cast 9570 | else if(tng_data->output_endianness_swap_func_32 == | ^~ mdtraj/formats/tng/src/lib/tng_io.c:9588:53: warning: comparison of distinct pointer types lacks a cast 9588 | if(tng_data->output_endianness_swap_func_64 == | ^~ mdtraj/formats/tng/src/lib/tng_io.c:9593:58: warning: comparison of distinct pointer types lacks a cast 9593 | else if(tng_data->output_endianness_swap_func_64 == | ^~ mdtraj/formats/tng/src/lib/tng_io.c: In function ‘tng_output_file_endianness_set’: mdtraj/formats/tng/src/lib/tng_io.c:9651:54: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int32_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint32_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, unsigned int *)’} [-Wincompatible-pointer-types] 9651 | tng_data->output_endianness_swap_func_32 = | ^ mdtraj/formats/tng/src/lib/tng_io.c:9660:54: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int64_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, long int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint64_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, long unsigned int *)’} [-Wincompatible-pointer-types] 9660 | tng_data->output_endianness_swap_func_64 = | ^ mdtraj/formats/tng/src/lib/tng_io.c:9673:54: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int32_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint32_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, unsigned int *)’} [-Wincompatible-pointer-types] 9673 | tng_data->output_endianness_swap_func_32 = | ^ mdtraj/formats/tng/src/lib/tng_io.c:9682:54: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int64_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, long int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint64_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, long unsigned int *)’} [-Wincompatible-pointer-types] 9682 | tng_data->output_endianness_swap_func_64 = | ^ In file included from /usr/include/string.h:519, from mdtraj/formats/tng/include/tng/tng_io.h:302, from mdtraj/formats/tng/src/lib/tng_io.c:20: In function ‘strncpy’, inlined from ‘tng_gen_data_block_add’ at mdtraj/formats/tng/src/lib/tng_io.c:12613:9: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:95:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-truncation] 95 | return __builtin___strncpy_chk (__dest, __src, __len, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 96 | __glibc_objsize (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/tng/src/lib/tng_io.c: In function ‘tng_gen_data_block_add’: mdtraj/formats/tng/src/lib/tng_io.c:12613:47: note: length computed here 12613 | strncpy(data->block_name, block_name, strlen(block_name) + 1); | ^~~~~~~~~~~~~~~~~~ mdtraj/formats/tng/src/lib/tng_io.c: In function ‘tng_data_block_write.isra’: mdtraj/formats/tng/src/lib/tng_io.c:5986:72: warning: ‘num_first_particle’ may be used uninitialized in this function [-Wmaybe-uninitialized] 5986 | for(j = num_first_particle; j < num_first_particle + n_particles; | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ mdtraj/formats/tng/src/lib/tng_io.c:4308:24: warning: ‘n_particles’ may be used uninitialized in this function [-Wmaybe-uninitialized] 4308 | dest = tng_compress_pos_float((float *)*data, (int)n_particles, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 4309 | (int)n_frames, | ~~~~~~~~~~~~~~ 4310 | f_precision, | ~~~~~~~~~~~~ 4311 | 0, alt_algo, | ~~~~~~~~~~~~ 4312 | &compressed_len); | ~~~~~~~~~~~~~~~~ mdtraj/formats/tng/src/lib/tng_io.c:5684:13: note: ‘n_particles’ was declared here 5684 | int64_t n_particles, num_first_particle, n_frames, stride_length; | ^~~~~~~~~~~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -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/python3.10 -c mdtraj/formats/tng/tng.c -o build/temp.linux-x86_64-3.10/mdtraj/formats/tng/tng.o In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 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:745: /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:3627:104: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 3627 | __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:3682:88: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 3682 | __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:3714:90: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 3714 | __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:3746:95: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 3746 | __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:3816:113: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 3816 | __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:3860:77: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 3860 | __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:4656:106: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 4656 | __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:4701:108: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 4701 | __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:4808:115: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 4808 | __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:4838:105: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 4838 | __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:4966:105: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 4966 | __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:5567:126: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 5567 | __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:5977:152: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 5977 | __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:6245:108: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 6245 | __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:6347:304: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 6347 | __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:8839:94: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 8839 | __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:8871:75: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 8871 | __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:8903:81: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 8903 | __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:9226:77: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 9226 | __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:9417:372: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 9417 | __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:9469:378: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 9469 | __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:9531:89: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 9531 | __pyx_t_1 = ((tng_frame_set_first_frame_time_set(__pyx_v_self->_traj, __pyx_t_15) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.10/mdtraj/formats/tng/src/compression/bwlzh.o build/temp.linux-x86_64-3.10/mdtraj/formats/tng/src/compression/bwt.o build/temp.linux-x86_64-3.10/mdtraj/formats/tng/src/compression/coder.o build/temp.linux-x86_64-3.10/mdtraj/formats/tng/src/compression/dict.o build/temp.linux-x86_64-3.10/mdtraj/formats/tng/src/compression/fixpoint.o build/temp.linux-x86_64-3.10/mdtraj/formats/tng/src/compression/huffman.o build/temp.linux-x86_64-3.10/mdtraj/formats/tng/src/compression/huffmem.o build/temp.linux-x86_64-3.10/mdtraj/formats/tng/src/compression/lz77.o build/temp.linux-x86_64-3.10/mdtraj/formats/tng/src/compression/merge_sort.o build/temp.linux-x86_64-3.10/mdtraj/formats/tng/src/compression/mtf.o build/temp.linux-x86_64-3.10/mdtraj/formats/tng/src/compression/rle.o build/temp.linux-x86_64-3.10/mdtraj/formats/tng/src/compression/tng_compress.o build/temp.linux-x86_64-3.10/mdtraj/formats/tng/src/compression/vals16.o build/temp.linux-x86_64-3.10/mdtraj/formats/tng/src/compression/warnmalloc.o build/temp.linux-x86_64-3.10/mdtraj/formats/tng/src/compression/widemuldiv.o build/temp.linux-x86_64-3.10/mdtraj/formats/tng/src/compression/xtc2.o build/temp.linux-x86_64-3.10/mdtraj/formats/tng/src/compression/xtc3.o build/temp.linux-x86_64-3.10/mdtraj/formats/tng/src/lib/md5.o build/temp.linux-x86_64-3.10/mdtraj/formats/tng/src/lib/tng_io.o build/temp.linux-x86_64-3.10/mdtraj/formats/tng/tng.o -lz -o /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/formats/tng.cpython-310-x86_64-linux-gnu.so building 'mdtraj.formats.dcd' extension creating build/temp.linux-x86_64-3.10/mdtraj/formats/dcd creating build/temp.linux-x86_64-3.10/mdtraj/formats/dcd/src x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -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/python3.10 -c mdtraj/formats/dcd/dcd.c -o build/temp.linux-x86_64-3.10/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:1969, 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:717: /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:631:40: warning: ‘__pyx_v_i’ may be used uninitialized in this function [-Wmaybe-uninitialized] 631 | #define PyInt_FromLong PyLong_FromLong | ^~~~~~~~~~~~~~~ mdtraj/formats/dcd/dcd.c:5369:7: note: ‘__pyx_v_i’ was declared here 5369 | int __pyx_v_i; | ^~~~~~~~~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -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/python3.10 -c mdtraj/formats/dcd/src/dcdplugin.c -o build/temp.linux-x86_64-3.10/mdtraj/formats/dcd/src/dcdplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.10/mdtraj/formats/dcd/dcd.o build/temp.linux-x86_64-3.10/mdtraj/formats/dcd/src/dcdplugin.o -o /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/formats/dcd.cpython-310-x86_64-linux-gnu.so building 'mdtraj.formats.binpos' extension creating build/temp.linux-x86_64-3.10/mdtraj/formats/binpos creating build/temp.linux-x86_64-3.10/mdtraj/formats/binpos/src x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -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/python3.10 -c mdtraj/formats/binpos/binpos.c -o build/temp.linux-x86_64-3.10/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:1969, 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:717: /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:5447:6: warning: ‘__pyx_v_status’ may be used uninitialized [-Wmaybe-uninitialized] 5447 | if (__pyx_t_2) { | ^ mdtraj/formats/binpos/binpos.c:4927:7: note: ‘__pyx_v_status’ was declared here 4927 | int __pyx_v_status; | ^~~~~~~~~~~~~~ mdtraj/formats/binpos/binpos.c:631:40: warning: ‘__pyx_v_i’ may be used uninitialized in this function [-Wmaybe-uninitialized] 631 | #define PyInt_FromLong PyLong_FromLong | ^~~~~~~~~~~~~~~ mdtraj/formats/binpos/binpos.c:4924:7: note: ‘__pyx_v_i’ was declared here 4924 | int __pyx_v_i; | ^~~~~~~~~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -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/python3.10 -c mdtraj/formats/binpos/src/binposplugin.c -o build/temp.linux-x86_64-3.10/mdtraj/formats/binpos/src/binposplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.10/mdtraj/formats/binpos/binpos.o build/temp.linux-x86_64-3.10/mdtraj/formats/binpos/src/binposplugin.o -o /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/formats/binpos.cpython-310-x86_64-linux-gnu.so building 'mdtraj.formats.dtr' extension creating build/temp.linux-x86_64-3.10/mdtraj/formats/dtr creating build/temp.linux-x86_64-3.10/mdtraj/formats/dtr/src x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -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/python3.10 -c mdtraj/formats/dtr/dtr.cpp -o build/temp.linux-x86_64-3.10/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:1969, 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:738: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -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/python3.10 -c mdtraj/formats/dtr/src/dtrplugin.cxx -o build/temp.linux-x86_64-3.10/mdtraj/formats/dtr/src/dtrplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/formats/dtr/src/dtrplugin.cxx: In member function ‘bool desres::molfile::Timekeys::init(const string&)’: mdtraj/formats/dtr/src/dtrplugin.cxx:487:27: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 487 | printf("size %d framesize %d\n\n", | ~^ | | | int | %ld 488 | keys[i].size(), m_framesize); | ~~~~~~~~~~~~~~ | | | uint64_t {aka long unsigned int} mdtraj/formats/dtr/src/dtrplugin.cxx:487:40: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 487 | printf("size %d framesize %d\n\n", | ~^ | | | int | %ld 488 | keys[i].size(), m_framesize); | ~~~~~~~~~~~ | | | uint64_t {aka long unsigned int} mdtraj/formats/dtr/src/dtrplugin.cxx: In constructor ‘{anonymous}::DDException::DDException(const string&, int)’: mdtraj/formats/dtr/src/dtrplugin.cxx:680:43: warning: ‘*this.{anonymous}::DDException::eno’ is used uninitialized [-Wuninitialized] 680 | : std::runtime_error(text + strerror(eno)), eno(_eno){} | ~~~~~~~~^~~~~ mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘void DDmkdir(const string&, mode_t, int, int)’: mdtraj/formats/dtr/src/dtrplugin.cxx:706:23: warning: ‘%03x’ directive writing between 3 and 8 bytes into a region of size 6 [-Wformat-overflow=] 706 | sprintf(sub, "%03x/", i); | ^~~~ mdtraj/formats/dtr/src/dtrplugin.cxx:706:22: note: directive argument in the range [0, 2147483646] 706 | sprintf(sub, "%03x/", i); | ^~~~~~~ In file included from /usr/include/stdio.h:866, from mdtraj/formats/dtr/include/molfile_plugin.h:35, from mdtraj/formats/dtr/include/dtrplugin.hxx:46, from mdtraj/formats/dtr/src/dtrplugin.cxx:42: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 5 and 10 bytes into a destination of size 6 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 40 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ mdtraj/formats/dtr/src/dtrplugin.cxx:714:30: warning: ‘%03x’ directive writing between 3 and 8 bytes into a region of size 6 [-Wformat-overflow=] 714 | sprintf(subsub, "%03x", j); | ^~~~ mdtraj/formats/dtr/src/dtrplugin.cxx:714:29: note: directive argument in the range [0, 2147483646] 714 | sprintf(subsub, "%03x", j); | ^~~~~~ In file included from /usr/include/stdio.h:866, from mdtraj/formats/dtr/include/molfile_plugin.h:35, from mdtraj/formats/dtr/include/dtrplugin.hxx:46, from mdtraj/formats/dtr/src/dtrplugin.cxx:42: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 4 and 9 bytes into a destination of size 6 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 40 | __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:667:35: 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:866, from mdtraj/formats/dtr/include/molfile_plugin.h:35, from mdtraj/formats/dtr/include/dtrplugin.hxx:46, from mdtraj/formats/dtr/src/dtrplugin.cxx:42: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 5 and 10 bytes into a destination of size 9 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 40 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ mdtraj/formats/dtr/src/dtrplugin.cxx:665:35: warning: ‘%03x’ directive writing between 3 and 8 bytes into a region of size between 0 and 5 [-Wformat-overflow=] 665 | sprintf(answer, "%03x/%03x/", d1, d2); | ^~~~ mdtraj/formats/dtr/src/dtrplugin.cxx:665:29: note: directive argument in the range [0, 2147483646] 665 | sprintf(answer, "%03x/%03x/", d1, d2); | ^~~~~~~~~~~~ In file included from /usr/include/stdio.h:866, from mdtraj/formats/dtr/include/molfile_plugin.h:35, from mdtraj/formats/dtr/include/dtrplugin.hxx:46, from mdtraj/formats/dtr/src/dtrplugin.cxx:42: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 9 and 19 bytes into a destination of size 9 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 40 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.10/mdtraj/formats/dtr/dtr.o build/temp.linux-x86_64-3.10/mdtraj/formats/dtr/src/dtrplugin.o -o /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/formats/dtr.cpython-310-x86_64-linux-gnu.so building 'mdtraj._rmsd' extension creating build/temp.linux-x86_64-3.10/mdtraj/rmsd creating build/temp.linux-x86_64-3.10/mdtraj/rmsd/src x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -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/python3.10 -c mdtraj/rmsd/_rmsd.cpp -o build/temp.linux-x86_64-3.10/mdtraj/rmsd/_rmsd.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -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/python3.10 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-x86_64-3.10/mdtraj/rmsd/src/center.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -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/python3.10 -c mdtraj/rmsd/src/rotation.cpp -o build/temp.linux-x86_64-3.10/mdtraj/rmsd/src/rotation.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -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/python3.10 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-x86_64-3.10/mdtraj/rmsd/src/theobald_rmsd.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.10/mdtraj/rmsd/_rmsd.o build/temp.linux-x86_64-3.10/mdtraj/rmsd/src/center.o build/temp.linux-x86_64-3.10/mdtraj/rmsd/src/rotation.o build/temp.linux-x86_64-3.10/mdtraj/rmsd/src/theobald_rmsd.o -lgomp -o /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/_rmsd.cpython-310-x86_64-linux-gnu.so building 'mdtraj._lprmsd' extension x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -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/python3.10 -c mdtraj/rmsd/_lprmsd.cpp -o build/temp.linux-x86_64-3.10/mdtraj/rmsd/_lprmsd.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 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:749: /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 ‘PyObject* __pyx_pf_6mdtraj_7_lprmsd_lprmsd(PyObject*, PyObject*, PyObject*, int, PyObject*, PyObject*, PyLongObject*, PyLongObject*)’: mdtraj/rmsd/_lprmsd.cpp:4021:14: 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] 4021 | } else if (unlikely(__pyx_t_34 >= __pyx_pybuffernd_ref_xyz_frame_dis.diminfo[0].shape)) __pyx_t_33 = 0; | ^~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -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/python3.10 -c mdtraj/rmsd/src/Munkres.cpp -o build/temp.linux-x86_64-3.10/mdtraj/rmsd/src/Munkres.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -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/python3.10 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-x86_64-3.10/mdtraj/rmsd/src/center.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -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/python3.10 -c mdtraj/rmsd/src/euclidean_permutation.cpp -o build/temp.linux-x86_64-3.10/mdtraj/rmsd/src/euclidean_permutation.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -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/python3.10 -c mdtraj/rmsd/src/fancy_index.cpp -o build/temp.linux-x86_64-3.10/mdtraj/rmsd/src/fancy_index.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -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/python3.10 -c mdtraj/rmsd/src/rotation.cpp -o build/temp.linux-x86_64-3.10/mdtraj/rmsd/src/rotation.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -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/python3.10 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-x86_64-3.10/mdtraj/rmsd/src/theobald_rmsd.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.10/mdtraj/rmsd/_lprmsd.o build/temp.linux-x86_64-3.10/mdtraj/rmsd/src/Munkres.o build/temp.linux-x86_64-3.10/mdtraj/rmsd/src/center.o build/temp.linux-x86_64-3.10/mdtraj/rmsd/src/euclidean_permutation.o build/temp.linux-x86_64-3.10/mdtraj/rmsd/src/fancy_index.o build/temp.linux-x86_64-3.10/mdtraj/rmsd/src/rotation.o build/temp.linux-x86_64-3.10/mdtraj/rmsd/src/theobald_rmsd.o -lgomp -o /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/_lprmsd.cpython-310-x86_64-linux-gnu.so building 'mdtraj.core.lib.libtheobald' extension x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -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/python3.10 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-x86_64-3.10/mdtraj/rmsd/src/theobald_rmsd.o -msse2 -mssse3 -O3 -funroll-loops --std=c++11 x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -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/python3.10 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-x86_64-3.10/mdtraj/rmsd/src/center.o -msse2 -mssse3 -O3 -funroll-loops --std=c++11 x86_64-linux-gnu-gcc-ar rcs /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/core/lib/libtheobald.a build/temp.linux-x86_64-3.10/mdtraj/rmsd/src/theobald_rmsd.o build/temp.linux-x86_64-3.10/mdtraj/rmsd/src/center.o building 'mdtraj.geometry._geometry' extension creating build/temp.linux-x86_64-3.10/mdtraj/geometry creating build/temp.linux-x86_64-3.10/mdtraj/geometry/src x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -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/python3.10 -c mdtraj/geometry/src/_geometry.cpp -o build/temp.linux-x86_64-3.10/mdtraj/geometry/src/_geometry.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 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:751: /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:6022:224: warning: ‘__pyx_v_delta[2]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 6022 | (__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:6036:277: warning: ‘__pyx_v_delta[1]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 6036 | (__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:6036:277: warning: ‘__pyx_v_offset[1]’ may be used uninitialized in this function [-Wmaybe-uninitialized] x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -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/python3.10 -c mdtraj/geometry/src/dssp.cpp -o build/temp.linux-x86_64-3.10/mdtraj/geometry/src/dssp.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -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/python3.10 -c mdtraj/geometry/src/geometry.cpp -o build/temp.linux-x86_64-3.10/mdtraj/geometry/src/geometry.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -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/python3.10 -c mdtraj/geometry/src/sasa.cpp -o build/temp.linux-x86_64-3.10/mdtraj/geometry/src/sasa.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.10/mdtraj/geometry/src/_geometry.o build/temp.linux-x86_64-3.10/mdtraj/geometry/src/dssp.o build/temp.linux-x86_64-3.10/mdtraj/geometry/src/geometry.o build/temp.linux-x86_64-3.10/mdtraj/geometry/src/sasa.o -lgomp -o /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/geometry/_geometry.cpython-310-x86_64-linux-gnu.so building 'mdtraj.geometry.drid' extension x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -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/python3.10 -c mdtraj/geometry/drid.cpp -o build/temp.linux-x86_64-3.10/mdtraj/geometry/drid.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -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/python3.10 -c mdtraj/geometry/src/dridkernels.cpp -o build/temp.linux-x86_64-3.10/mdtraj/geometry/src/dridkernels.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -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/python3.10 -c mdtraj/geometry/src/moments.cpp -o build/temp.linux-x86_64-3.10/mdtraj/geometry/src/moments.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.10/mdtraj/geometry/drid.o build/temp.linux-x86_64-3.10/mdtraj/geometry/src/dridkernels.o build/temp.linux-x86_64-3.10/mdtraj/geometry/src/moments.o -lgomp -o /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/geometry/drid.cpython-310-x86_64-linux-gnu.so building 'mdtraj.geometry.neighbors' extension x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -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/python3.10 -c mdtraj/geometry/neighbors.cpp -o build/temp.linux-x86_64-3.10/mdtraj/geometry/neighbors.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -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/python3.10 -c mdtraj/geometry/src/neighbors.cpp -o build/temp.linux-x86_64-3.10/mdtraj/geometry/src/neighbors.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.10/mdtraj/geometry/neighbors.o build/temp.linux-x86_64-3.10/mdtraj/geometry/src/neighbors.o -lgomp -o /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/geometry/neighbors.cpython-310-x86_64-linux-gnu.so building 'mdtraj.geometry.neighborlist' extension x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -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/python3.10 -c mdtraj/geometry/neighborlist.cpp -o build/temp.linux-x86_64-3.10/mdtraj/geometry/neighborlist.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -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/python3.10 -c mdtraj/geometry/src/neighborlist.cpp -o build/temp.linux-x86_64-3.10/mdtraj/geometry/src/neighborlist.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In constructor ‘Voxels::Voxels(float, float, float, float, float, float, const float (&)[3][3], bool)’, inlined from ‘std::vector > _compute_neighborlist(const float*, int, float, const float*)’ at mdtraj/geometry/src/neighborlist.cpp:377:116: mdtraj/geometry/src/neighborlist.cpp:50:53: warning: ‘periodicBoxVectors’ may be used uninitialized [-Wmaybe-uninitialized] 50 | periodicBoxSize[0] = periodicBoxVectors[0][0]; | ~~~~~~~~~~~~~~~~~~~~~~~^ mdtraj/geometry/src/neighborlist.cpp: In function ‘std::vector > _compute_neighborlist(const float*, int, float, const float*)’: mdtraj/geometry/src/neighborlist.cpp:341:11: note: ‘periodicBoxVectors’ declared here 341 | float periodicBoxVectors[3][3]; | ^~~~~~~~~~~~~~~~~~ In constructor ‘Voxels::Voxels(float, float, float, float, float, float, const float (&)[3][3], bool)’, inlined from ‘std::vector > _compute_neighborlist(const float*, int, float, const float*)’ at mdtraj/geometry/src/neighborlist.cpp:377:116: mdtraj/geometry/src/neighborlist.cpp:56:45: warning: ‘periodicBoxVectors’ may be used uninitialized [-Wmaybe-uninitialized] 56 | triclinic = (periodicBoxVectors[0][1] != 0.0 || periodicBoxVectors[0][2] != 0.0 || | ~~~~~~~~~~~~~~~~~~~~~~~^ mdtraj/geometry/src/neighborlist.cpp: In function ‘std::vector > _compute_neighborlist(const float*, int, float, const float*)’: mdtraj/geometry/src/neighborlist.cpp:341:11: note: ‘periodicBoxVectors’ declared here 341 | float periodicBoxVectors[3][3]; | ^~~~~~~~~~~~~~~~~~ mdtraj/geometry/src/neighborlist.cpp:374:49: warning: ‘periodicBoxVectors’ may be used uninitialized [-Wmaybe-uninitialized] 374 | edgeSizeY = 0.6f*periodicBoxVectors[1][1]/floorf(periodicBoxVectors[1][1]/maxDistance); | ~~~~~~~~~~~~~~~~~~~~~~~^ mdtraj/geometry/src/neighborlist.cpp:341:11: note: ‘periodicBoxVectors’ declared here 341 | float periodicBoxVectors[3][3]; | ^~~~~~~~~~~~~~~~~~ mdtraj/geometry/src/neighborlist.cpp:375:49: warning: ‘periodicBoxVectors’ may be used uninitialized [-Wmaybe-uninitialized] 375 | edgeSizeZ = 0.6f*periodicBoxVectors[2][2]/floorf(periodicBoxVectors[2][2]/maxDistance); | ~~~~~~~~~~~~~~~~~~~~~~~^ mdtraj/geometry/src/neighborlist.cpp:341:11: note: ‘periodicBoxVectors’ declared here 341 | float periodicBoxVectors[3][3]; | ^~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/mdtraj-X0NYWR/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.10/mdtraj/geometry/neighborlist.o build/temp.linux-x86_64-3.10/mdtraj/geometry/src/neighborlist.o -lgomp -o /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/geometry/neighborlist.cpython-310-x86_64-linux-gnu.so cp -a /build/mdtraj-X0NYWR/mdtraj-1.9.7/examples /build/mdtraj-X0NYWR/mdtraj-1.9.7/examples.orig mkdir -p /build/mdtraj-X0NYWR/mdtraj-1.9.7/build/html/examples/iterload ln -s /build/mdtraj-X0NYWR/mdtraj-1.9.7/examples/data /build/mdtraj-X0NYWR/mdtraj-1.9.7/build/html/examples/iterload/data sed "s|http://www.rcsb.org/pdb/files|/build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/external|g" -i /build/mdtraj-X0NYWR/mdtraj-1.9.7/examples/*.ipynb PYTHONPATH=/build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build \ MPLCONFIGDIR=/build/mdtraj-X0NYWR/mdtraj-1.9.7/build/matplotlib \ make -C docs BUILDDIR=/build/mdtraj-X0NYWR/mdtraj-1.9.7/build html make[2]: Entering directory '/build/mdtraj-X0NYWR/mdtraj-1.9.7/docs' sphinx-build -b html -d /build/mdtraj-X0NYWR/mdtraj-1.9.7/build/doctrees . /build/mdtraj-X0NYWR/mdtraj-1.9.7/build/html Running Sphinx v4.5.0 [autosummary] generating autosummary for: analysis.rst, api/reporters.rst, api/trajectory_files.rst, api/utils.rst, atom_selection.rst, building_docs.rst, examples/atom-selection.rst, examples/centroids.rst, examples/clustering.rst, examples/hbonds.rst, ..., examples/solvent-accessible-surface-area.rst, examples/two-pass-clustering.rst, faq.rst, hdf5_format.rst, index.rst, installation.rst, load_functions.rst, mdconvert.rst, new_to_python.rst, whatsnew.rst [autosummary] generating autosummary for: /build/mdtraj-X0NYWR/mdtraj-1.9.7/docs/api/generated/mdtraj.Topology.rst, /build/mdtraj-X0NYWR/mdtraj-1.9.7/docs/api/generated/mdtraj.Trajectory.rst, /build/mdtraj-X0NYWR/mdtraj-1.9.7/docs/api/generated/mdtraj.Trajectory.superpose.rst, /build/mdtraj-X0NYWR/mdtraj-1.9.7/docs/api/generated/mdtraj.acylindricity.rst, /build/mdtraj-X0NYWR/mdtraj-1.9.7/docs/api/generated/mdtraj.asphericity.rst, /build/mdtraj-X0NYWR/mdtraj-1.9.7/docs/api/generated/mdtraj.baker_hubbard.rst, /build/mdtraj-X0NYWR/mdtraj-1.9.7/docs/api/generated/mdtraj.chemical_shifts_ppm.rst, /build/mdtraj-X0NYWR/mdtraj-1.9.7/docs/api/generated/mdtraj.chemical_shifts_shiftx2.rst, /build/mdtraj-X0NYWR/mdtraj-1.9.7/docs/api/generated/mdtraj.chemical_shifts_spartaplus.rst, /build/mdtraj-X0NYWR/mdtraj-1.9.7/docs/api/generated/mdtraj.compute_J3_HN_C.rst, ..., /build/mdtraj-X0NYWR/mdtraj-1.9.7/docs/api/generated/mdtraj.utils.check_random_state.rst, /build/mdtraj-X0NYWR/mdtraj-1.9.7/docs/api/generated/mdtraj.utils.ensure_type.rst, /build/mdtraj-X0NYWR/mdtraj-1.9.7/docs/api/generated/mdtraj.utils.ilen.rst, /build/mdtraj-X0NYWR/mdtraj-1.9.7/docs/api/generated/mdtraj.utils.import_.rst, /build/mdtraj-X0NYWR/mdtraj-1.9.7/docs/api/generated/mdtraj.utils.in_units_of.rst, /build/mdtraj-X0NYWR/mdtraj-1.9.7/docs/api/generated/mdtraj.utils.lengths_and_angles_to_box_vectors.rst, /build/mdtraj-X0NYWR/mdtraj-1.9.7/docs/api/generated/mdtraj.utils.rotation_matrix_from_quaternion.rst, /build/mdtraj-X0NYWR/mdtraj-1.9.7/docs/api/generated/mdtraj.utils.timing.rst, /build/mdtraj-X0NYWR/mdtraj-1.9.7/docs/api/generated/mdtraj.utils.uniform_quaternion.rst, /build/mdtraj-X0NYWR/mdtraj-1.9.7/docs/api/generated/mdtraj.wernet_nilsson.rst building [mo]: targets for 0 po files that are out of date building [html]: targets for 29 source files that are out of date updating environment: [new config] 127 added, 0 changed, 0 removed reading sources... [ 0%] analysis reading sources... [ 1%] api/generated/mdtraj.Topology /usr/lib/python3/dist-packages/numpydoc/docscrape.py:440: UserWarning: potentially wrong underline length... Returns ---------- in Get the indices of biologically-relevant groups by name. ... in the docstring of select_atom_indices in /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/core/topology.py. warn(msg) /usr/lib/python3/dist-packages/numpydoc/docscrape.py:440: UserWarning: potentially wrong underline length... Returns ---------- in Get the indices of biologically-relevant groups by name. ... in the docstring of select_atom_indices in /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/core/topology.py. warn(msg) reading sources... [ 2%] api/generated/mdtraj.Trajectory reading sources... [ 3%] api/generated/mdtraj.Trajectory.superpose reading sources... [ 3%] api/generated/mdtraj.acylindricity reading sources... [ 4%] api/generated/mdtraj.asphericity reading sources... [ 5%] api/generated/mdtraj.baker_hubbard reading sources... [ 6%] api/generated/mdtraj.chemical_shifts_ppm reading sources... [ 7%] api/generated/mdtraj.chemical_shifts_shiftx2 reading sources... [ 7%] api/generated/mdtraj.chemical_shifts_spartaplus reading sources... [ 8%] api/generated/mdtraj.compute_J3_HN_C reading sources... [ 9%] api/generated/mdtraj.compute_J3_HN_CB reading sources... [ 10%] api/generated/mdtraj.compute_J3_HN_HA reading sources... [ 11%] api/generated/mdtraj.compute_angles reading sources... [ 11%] api/generated/mdtraj.compute_center_of_mass reading sources... [ 12%] api/generated/mdtraj.compute_chi1 reading sources... [ 13%] api/generated/mdtraj.compute_chi2 reading sources... [ 14%] api/generated/mdtraj.compute_chi3 reading sources... [ 14%] api/generated/mdtraj.compute_chi4 reading sources... [ 15%] api/generated/mdtraj.compute_contacts reading sources... [ 16%] api/generated/mdtraj.compute_dihedrals reading sources... [ 17%] api/generated/mdtraj.compute_directors reading sources... [ 18%] api/generated/mdtraj.compute_displacements reading sources... [ 18%] api/generated/mdtraj.compute_distances reading sources... [ 19%] api/generated/mdtraj.compute_drid reading sources... [ 20%] api/generated/mdtraj.compute_dssp reading sources... [ 21%] api/generated/mdtraj.compute_gyration_tensor reading sources... [ 22%] api/generated/mdtraj.compute_inertia_tensor reading sources... [ 22%] api/generated/mdtraj.compute_neighbors reading sources... [ 23%] api/generated/mdtraj.compute_nematic_order reading sources... [ 24%] api/generated/mdtraj.compute_omega reading sources... [ 25%] api/generated/mdtraj.compute_phi reading sources... [ 25%] api/generated/mdtraj.compute_psi reading sources... [ 26%] api/generated/mdtraj.compute_rdf reading sources... [ 27%] api/generated/mdtraj.compute_rg reading sources... [ 28%] api/generated/mdtraj.density reading sources... [ 29%] api/generated/mdtraj.dipole_moments reading sources... [ 29%] api/generated/mdtraj.formats.AmberNetCDFRestartFile reading sources... [ 30%] api/generated/mdtraj.formats.AmberRestartFile reading sources... [ 31%] api/generated/mdtraj.formats.ArcTrajectoryFile reading sources... [ 32%] api/generated/mdtraj.formats.BINPOSTrajectoryFile reading sources... [ 33%] api/generated/mdtraj.formats.DCDTrajectoryFile reading sources... [ 33%] api/generated/mdtraj.formats.DTRTrajectoryFile reading sources... [ 34%] api/generated/mdtraj.formats.GroTrajectoryFile reading sources... [ 35%] api/generated/mdtraj.formats.HDF5TrajectoryFile reading sources... [ 36%] api/generated/mdtraj.formats.LAMMPSTrajectoryFile reading sources... [ 37%] api/generated/mdtraj.formats.LH5TrajectoryFile reading sources... [ 37%] api/generated/mdtraj.formats.MDCRDTrajectoryFile reading sources... [ 38%] api/generated/mdtraj.formats.NetCDFTrajectoryFile reading sources... [ 39%] api/generated/mdtraj.formats.PDBTrajectoryFile reading sources... [ 40%] api/generated/mdtraj.formats.TRRTrajectoryFile reading sources... [ 40%] api/generated/mdtraj.formats.XTCTrajectoryFile reading sources... [ 41%] api/generated/mdtraj.formats.XYZTrajectoryFile reading sources... [ 42%] api/generated/mdtraj.geometry.squareform reading sources... [ 43%] api/generated/mdtraj.isothermal_compressability_kappa_T reading sources... [ 44%] api/generated/mdtraj.iterload reading sources... [ 44%] api/generated/mdtraj.join reading sources... [ 45%] api/generated/mdtraj.kabsch_sander reading sources... [ 46%] api/generated/mdtraj.load reading sources... [ 47%] api/generated/mdtraj.load_arc reading sources... [ 48%] api/generated/mdtraj.load_binpos reading sources... [ 48%] api/generated/mdtraj.load_dcd reading sources... [ 49%] api/generated/mdtraj.load_dtr reading sources... [ 50%] api/generated/mdtraj.load_frame reading sources... [ 51%] api/generated/mdtraj.load_hdf5 reading sources... [ 51%] api/generated/mdtraj.load_hoomdxml reading sources... [ 52%] api/generated/mdtraj.load_lammpstrj reading sources... [ 53%] api/generated/mdtraj.load_lh5 reading sources... [ 54%] api/generated/mdtraj.load_netcdf reading sources... [ 55%] api/generated/mdtraj.load_pdb reading sources... [ 55%] api/generated/mdtraj.load_prmtop reading sources... [ 56%] api/generated/mdtraj.load_trr reading sources... [ 57%] api/generated/mdtraj.load_xml reading sources... [ 58%] api/generated/mdtraj.load_xtc reading sources... [ 59%] api/generated/mdtraj.load_xyz reading sources... [ 59%] api/generated/mdtraj.lprmsd reading sources... [ 60%] api/generated/mdtraj.open reading sources... [ 61%] api/generated/mdtraj.principal_moments reading sources... [ 62%] api/generated/mdtraj.reindex_dataframe_by_atoms reading sources... [ 62%] api/generated/mdtraj.relative_shape_antisotropy reading sources... [ 63%] api/generated/mdtraj.reporters.DCDReporter reading sources... [ 64%] api/generated/mdtraj.reporters.HDF5Reporter reading sources... [ 65%] api/generated/mdtraj.reporters.NetCDFReporter reading sources... [ 66%] api/generated/mdtraj.rmsd reading sources... [ 66%] api/generated/mdtraj.rmsf reading sources... [ 67%] api/generated/mdtraj.shrake_rupley reading sources... [ 68%] api/generated/mdtraj.static_dielectric reading sources... [ 69%] api/generated/mdtraj.thermal_expansion_alpha_P reading sources... [ 70%] api/generated/mdtraj.utils.box_vectors_to_lengths_and_angles reading sources... [ 70%] api/generated/mdtraj.utils.check_random_state reading sources... [ 71%] api/generated/mdtraj.utils.ensure_type reading sources... [ 72%] api/generated/mdtraj.utils.ilen reading sources... [ 73%] api/generated/mdtraj.utils.import_ reading sources... [ 74%] api/generated/mdtraj.utils.in_units_of reading sources... [ 74%] api/generated/mdtraj.utils.lengths_and_angles_to_box_vectors reading sources... [ 75%] api/generated/mdtraj.utils.rotation_matrix_from_quaternion reading sources... [ 76%] api/generated/mdtraj.utils.timing reading sources... [ 77%] api/generated/mdtraj.utils.uniform_quaternion reading sources... [ 77%] api/generated/mdtraj.wernet_nilsson reading sources... [ 78%] api/reporters reading sources... [ 79%] api/trajectory_files reading sources... [ 80%] api/utils reading sources... [ 81%] atom_selection reading sources... [ 81%] building_docs reading sources... [ 82%] examples/atom-selection reading sources... [ 83%] examples/centroids reading sources... [ 84%] examples/clustering reading sources... [ 85%] examples/hbonds reading sources... [ 85%] examples/index reading sources... [ 86%] examples/introduction reading sources... [ 87%] examples/iterload reading sources... [ 88%] examples/native-contact reading sources... [ 88%] examples/nmr reading sources... [ 89%] examples/openmm reading sources... [ 90%] examples/pca reading sources... [ 91%] examples/ramachandran-plot reading sources... [ 92%] examples/rmsd-benchmark reading sources... [ 92%] examples/solvent-accessible-surface-area reading sources... [ 93%] examples/two-pass-clustering reading sources... [ 94%] faq reading sources... [ 95%] hdf5_format reading sources... [ 96%] index reading sources... [ 96%] installation reading sources... [ 97%] load_functions reading sources... [ 98%] mdconvert reading sources... [ 99%] new_to_python reading sources... [100%] whatsnew /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/geometry/shape.py:docstring of mdtraj.geometry.shape.asphericity:9: WARNING: Block quote ends without a blank line; unexpected unindent. /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_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/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/geometry/contact.py:docstring of mdtraj.geometry.contact.compute_contacts:36: ERROR: Unexpected indentation. /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/geometry/contact.py:docstring of mdtraj.geometry.contact.compute_contacts:45: WARNING: Block quote ends without a blank line; unexpected unindent. docstring of mdtraj.formats.dtr.load_dtr:7: ERROR: Unexpected indentation. /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/geometry/shape.py:docstring of mdtraj.geometry.shape.relative_shape_anisotropy:9: WARNING: Block quote ends without a blank line; unexpected unindent. docstring of mdtraj._rmsd.rmsf:46: WARNING: Block quote ends without a blank line; unexpected unindent. /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/utils/rotation.py:docstring of mdtraj.utils.rotation.uniform_quaternion:37: ERROR: Error in "rubric" directive: no content permitted. .. rubric:: References .. [R17e8d31e726c-1] K. Shoemake. Uniform random rotations. In D. Kirk, editor, Graphics Gems III, pages 124-132. Academic, New York, 1992. .. [R17e8d31e726c-2] http://planning.cs.uiuc.edu/node198.html /build/mdtraj-X0NYWR/mdtraj-1.9.7/docs/examples/atom-selection.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/atom-selection.ipynb :skip_exceptions: /build/mdtraj-X0NYWR/mdtraj-1.9.7/docs/examples/centroids.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/centroids.ipynb :skip_exceptions: /build/mdtraj-X0NYWR/mdtraj-1.9.7/docs/examples/clustering.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/clustering.ipynb :skip_exceptions: /build/mdtraj-X0NYWR/mdtraj-1.9.7/docs/examples/hbonds.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/hbonds.ipynb :skip_exceptions: /build/mdtraj-X0NYWR/mdtraj-1.9.7/docs/examples/iterload.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/iterload.ipynb :skip_exceptions: /build/mdtraj-X0NYWR/mdtraj-1.9.7/docs/examples/native-contact.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/native-contact.ipynb :skip_exceptions: /build/mdtraj-X0NYWR/mdtraj-1.9.7/docs/examples/nmr.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/nmr.ipynb :skip_exceptions: /build/mdtraj-X0NYWR/mdtraj-1.9.7/docs/examples/openmm.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/simulation-with-openmm.ipynb :skip_exceptions: /build/mdtraj-X0NYWR/mdtraj-1.9.7/docs/examples/pca.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/principal-components.ipynb :skip_exceptions: /build/mdtraj-X0NYWR/mdtraj-1.9.7/docs/examples/ramachandran-plot.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/ramachandran-plot.ipynb :skip_exceptions: /build/mdtraj-X0NYWR/mdtraj-1.9.7/docs/examples/rmsd-benchmark.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/rmsd-benchmark.ipynb :skip_exceptions: /build/mdtraj-X0NYWR/mdtraj-1.9.7/docs/examples/solvent-accessible-surface-area.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/solvent-accessible-surface-area.ipynb :skip_exceptions: /build/mdtraj-X0NYWR/mdtraj-1.9.7/docs/examples/two-pass-clustering.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/two-pass-clustering.ipynb :skip_exceptions: /build/mdtraj-X0NYWR/mdtraj-1.9.7/docs/installation.rst:1: WARNING: malformed hyperlink target. /build/mdtraj-X0NYWR/mdtraj-1.9.7/docs/mdconvert.rst:2: WARNING: Title underline too short. ``mdconvert`` (``mdconvert-mdtraj``) ============= /build/mdtraj-X0NYWR/mdtraj-1.9.7/docs/whatsnew.rst:7: WARNING: Title underline too short. v1.9.7 (November 12, 2021) ----------------------- looking for now-outdated files... none found pickling environment... done checking consistency... /build/mdtraj-X0NYWR/mdtraj-1.9.7/docs/building_docs.rst: WARNING: document isn't included in any toctree /build/mdtraj-X0NYWR/mdtraj-1.9.7/docs/faq.rst: WARNING: document isn't included in any toctree done preparing documents... done writing output... [ 0%] analysis writing output... [ 1%] api/generated/mdtraj.Topology writing output... [ 2%] api/generated/mdtraj.Trajectory writing output... [ 3%] api/generated/mdtraj.Trajectory.superpose writing output... [ 3%] api/generated/mdtraj.acylindricity writing output... [ 4%] api/generated/mdtraj.asphericity writing output... [ 5%] api/generated/mdtraj.baker_hubbard writing output... [ 6%] api/generated/mdtraj.chemical_shifts_ppm writing output... [ 7%] api/generated/mdtraj.chemical_shifts_shiftx2 writing output... [ 7%] api/generated/mdtraj.chemical_shifts_spartaplus writing output... [ 8%] api/generated/mdtraj.compute_J3_HN_C writing output... [ 9%] api/generated/mdtraj.compute_J3_HN_CB writing output... [ 10%] api/generated/mdtraj.compute_J3_HN_HA writing output... [ 11%] api/generated/mdtraj.compute_angles writing output... [ 11%] api/generated/mdtraj.compute_center_of_mass writing output... [ 12%] api/generated/mdtraj.compute_chi1 writing output... [ 13%] api/generated/mdtraj.compute_chi2 writing output... [ 14%] api/generated/mdtraj.compute_chi3 writing output... [ 14%] api/generated/mdtraj.compute_chi4 writing output... [ 15%] api/generated/mdtraj.compute_contacts writing output... [ 16%] api/generated/mdtraj.compute_dihedrals writing output... [ 17%] api/generated/mdtraj.compute_directors writing output... [ 18%] api/generated/mdtraj.compute_displacements writing output... [ 18%] api/generated/mdtraj.compute_distances writing output... [ 19%] api/generated/mdtraj.compute_drid writing output... [ 20%] api/generated/mdtraj.compute_dssp writing output... [ 21%] api/generated/mdtraj.compute_gyration_tensor writing output... [ 22%] api/generated/mdtraj.compute_inertia_tensor writing output... [ 22%] api/generated/mdtraj.compute_neighbors writing output... [ 23%] api/generated/mdtraj.compute_nematic_order writing output... [ 24%] api/generated/mdtraj.compute_omega writing output... [ 25%] api/generated/mdtraj.compute_phi writing output... [ 25%] api/generated/mdtraj.compute_psi writing output... [ 26%] api/generated/mdtraj.compute_rdf writing output... [ 27%] api/generated/mdtraj.compute_rg writing output... [ 28%] api/generated/mdtraj.density writing output... [ 29%] api/generated/mdtraj.dipole_moments writing output... [ 29%] api/generated/mdtraj.formats.AmberNetCDFRestartFile writing output... [ 30%] api/generated/mdtraj.formats.AmberRestartFile writing output... [ 31%] api/generated/mdtraj.formats.ArcTrajectoryFile writing output... [ 32%] api/generated/mdtraj.formats.BINPOSTrajectoryFile writing output... [ 33%] api/generated/mdtraj.formats.DCDTrajectoryFile writing output... [ 33%] api/generated/mdtraj.formats.DTRTrajectoryFile writing output... [ 34%] api/generated/mdtraj.formats.GroTrajectoryFile writing output... [ 35%] api/generated/mdtraj.formats.HDF5TrajectoryFile writing output... [ 36%] api/generated/mdtraj.formats.LAMMPSTrajectoryFile writing output... [ 37%] api/generated/mdtraj.formats.LH5TrajectoryFile writing output... [ 37%] api/generated/mdtraj.formats.MDCRDTrajectoryFile writing output... [ 38%] api/generated/mdtraj.formats.NetCDFTrajectoryFile writing output... [ 39%] api/generated/mdtraj.formats.PDBTrajectoryFile writing output... [ 40%] api/generated/mdtraj.formats.TRRTrajectoryFile writing output... [ 40%] api/generated/mdtraj.formats.XTCTrajectoryFile writing output... [ 41%] api/generated/mdtraj.formats.XYZTrajectoryFile writing output... [ 42%] api/generated/mdtraj.geometry.squareform writing output... [ 43%] api/generated/mdtraj.isothermal_compressability_kappa_T writing output... [ 44%] api/generated/mdtraj.iterload writing output... [ 44%] api/generated/mdtraj.join writing output... [ 45%] api/generated/mdtraj.kabsch_sander writing output... [ 46%] api/generated/mdtraj.load writing output... [ 47%] api/generated/mdtraj.load_arc writing output... [ 48%] api/generated/mdtraj.load_binpos writing output... [ 48%] api/generated/mdtraj.load_dcd writing output... [ 49%] api/generated/mdtraj.load_dtr writing output... [ 50%] api/generated/mdtraj.load_frame writing output... [ 51%] api/generated/mdtraj.load_hdf5 writing output... [ 51%] api/generated/mdtraj.load_hoomdxml writing output... [ 52%] api/generated/mdtraj.load_lammpstrj writing output... [ 53%] api/generated/mdtraj.load_lh5 writing output... [ 54%] api/generated/mdtraj.load_netcdf writing output... [ 55%] api/generated/mdtraj.load_pdb writing output... [ 55%] api/generated/mdtraj.load_prmtop writing output... [ 56%] api/generated/mdtraj.load_trr writing output... [ 57%] api/generated/mdtraj.load_xml writing output... [ 58%] api/generated/mdtraj.load_xtc writing output... [ 59%] api/generated/mdtraj.load_xyz writing output... [ 59%] api/generated/mdtraj.lprmsd writing output... [ 60%] api/generated/mdtraj.open writing output... [ 61%] api/generated/mdtraj.principal_moments writing output... [ 62%] api/generated/mdtraj.reindex_dataframe_by_atoms writing output... [ 62%] api/generated/mdtraj.relative_shape_antisotropy writing output... [ 63%] api/generated/mdtraj.reporters.DCDReporter writing output... [ 64%] api/generated/mdtraj.reporters.HDF5Reporter writing output... [ 65%] api/generated/mdtraj.reporters.NetCDFReporter writing output... [ 66%] api/generated/mdtraj.rmsd writing output... [ 66%] api/generated/mdtraj.rmsf writing output... [ 67%] api/generated/mdtraj.shrake_rupley writing output... [ 68%] api/generated/mdtraj.static_dielectric writing output... [ 69%] api/generated/mdtraj.thermal_expansion_alpha_P writing output... [ 70%] api/generated/mdtraj.utils.box_vectors_to_lengths_and_angles writing output... [ 70%] api/generated/mdtraj.utils.check_random_state writing output... [ 71%] api/generated/mdtraj.utils.ensure_type writing output... [ 72%] api/generated/mdtraj.utils.ilen writing output... [ 73%] api/generated/mdtraj.utils.import_ writing output... [ 74%] api/generated/mdtraj.utils.in_units_of writing output... [ 74%] api/generated/mdtraj.utils.lengths_and_angles_to_box_vectors writing output... [ 75%] api/generated/mdtraj.utils.rotation_matrix_from_quaternion writing output... [ 76%] api/generated/mdtraj.utils.timing writing output... [ 77%] api/generated/mdtraj.utils.uniform_quaternion writing output... [ 77%] api/generated/mdtraj.wernet_nilsson writing output... [ 78%] api/reporters writing output... [ 79%] api/trajectory_files writing output... [ 80%] api/utils writing output... [ 81%] atom_selection writing output... [ 81%] building_docs writing output... [ 82%] examples/atom-selection writing output... [ 83%] examples/centroids writing output... [ 84%] examples/clustering writing output... [ 85%] examples/hbonds writing output... [ 85%] examples/index writing output... [ 86%] examples/introduction writing output... [ 87%] examples/iterload writing output... [ 88%] examples/native-contact writing output... [ 88%] examples/nmr writing output... [ 89%] examples/openmm writing output... [ 90%] examples/pca writing output... [ 91%] examples/ramachandran-plot writing output... [ 92%] examples/rmsd-benchmark writing output... [ 92%] examples/solvent-accessible-surface-area writing output... [ 93%] examples/two-pass-clustering writing output... [ 94%] faq writing output... [ 95%] hdf5_format writing output... [ 96%] index writing output... [ 96%] installation writing output... [ 97%] load_functions writing output... [ 98%] mdconvert writing output... [ 99%] new_to_python writing output... [100%] whatsnew generating indices... genindex done writing additional pages... search done copying static files... done copying extra files... done dumping search index in English (code: en)... done dumping object inventory... done build succeeded, 26 warnings. The HTML pages are in ../build/html. Build finished. The HTML pages are in /build/mdtraj-X0NYWR/mdtraj-1.9.7/build/html. make[2]: Leaving directory '/build/mdtraj-X0NYWR/mdtraj-1.9.7/docs' for img in `find /build/mdtraj-X0NYWR/mdtraj-1.9.7/build/html/examples -name *.png`; do \ mv $img /build/mdtraj-X0NYWR/mdtraj-1.9.7/build/html/examples; \ done sed "s|/build/mdtraj-X0NYWR/mdtraj-1.9.7/build/html/examples/|./|g; s|.ipynb|.ipynb.gz|g" -i /build/mdtraj-X0NYWR/mdtraj-1.9.7/build/html/examples/*.html sed "s|/build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/external|http://www.rcsb.org/pdb/files|g" -i /build/mdtraj-X0NYWR/mdtraj-1.9.7/build/html/examples/*.html rm /build/mdtraj-X0NYWR/mdtraj-1.9.7/build/html/examples/iterload/data rm -rf /build/mdtraj-X0NYWR/mdtraj-1.9.7/examples mv /build/mdtraj-X0NYWR/mdtraj-1.9.7/examples.orig /build/mdtraj-X0NYWR/mdtraj-1.9.7/examples make[1]: Leaving directory '/build/mdtraj-X0NYWR/mdtraj-1.9.7' dh: command-omitted: The call to "dh_auto_test -i -O--buildsystem=pybuild" was omitted due to "DEB_BUILD_OPTIONS=nocheck" create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary-indep dh binary-indep --with python3,sphinxdoc --buildsystem=pybuild dh_testroot -i -O--buildsystem=pybuild dh_prep -i -O--buildsystem=pybuild dh_installdirs -i -O--buildsystem=pybuild dh_auto_install -i -O--buildsystem=pybuild I: pybuild base:237: /usr/bin/python3.9 setup.py install --root /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj Using built-in specs. COLLECT_GCC=/usr/bin/x86_64-linux-gnu-gcc COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/11/lto-wrapper OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa OFFLOAD_TARGET_DEFAULT=1 Target: x86_64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 11.2.0-19' --with-bugurl=file:///usr/share/doc/gcc-11/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-11 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --enable-cet --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/gcc-11-uiwEqG/gcc-11-11.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-11-uiwEqG/gcc-11-11.2.0/debian/tmp-gcn/usr --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=2 Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 11.2.0 (Debian 11.2.0-19) 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 /usr/lib/python3/dist-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. warnings.warn( running build running build_py copying mdtraj/version.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj running build_ext running install_lib creating /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj creating /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr creating /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib creating /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9 creating /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages creating /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/__init__.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/io.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj creating /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/core copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/core/__init__.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/core copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/core/element.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/core copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/core/residue_names.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/core copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/core/selection.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/core copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/core/topology.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/core copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/core/trajectory.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/core creating /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/core/lib copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/core/lib/libtheobald.a -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/core/lib copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/core/lib/theobald_rmsd.h -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/core/lib copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/core/lib/center.h -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/core/lib creating /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/__init__.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/amberrst.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/arc.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/gro.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/gsd.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/hdf5.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/hoomdxml.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/lammpstrj.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/lh5.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/mdcrd.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/mol2.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/netcdf.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/openmmxml.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/prmtop.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/psf.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/registry.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/xyzfile.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats creating /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/pdb copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/pdb/__init__.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/pdb copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/pdb/pdbfile.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/pdb copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/pdb/pdbstructure.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/pdb creating /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/pdb/data copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/pdb/data/pdbNames.xml -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/pdb/data copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/pdb/data/residues.xml -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/pdb/data copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/xtc.cpython-39-x86_64-linux-gnu.so -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/trr.cpython-39-x86_64-linux-gnu.so -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/tng.cpython-39-x86_64-linux-gnu.so -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/dcd.cpython-39-x86_64-linux-gnu.so -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/binpos.cpython-39-x86_64-linux-gnu.so -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/dtr.cpython-39-x86_64-linux-gnu.so -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats creating /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/__init__.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/alignment.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/angle.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/contact.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/dihedral.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/distance.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/dssp.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/hbond.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/internal.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/order.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/rdf.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/rg.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/sasa.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/shape.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/thermodynamic_properties.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/_geometry.cpython-39-x86_64-linux-gnu.so -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/drid.cpython-39-x86_64-linux-gnu.so -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/neighbors.cpython-39-x86_64-linux-gnu.so -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/neighborlist.cpython-39-x86_64-linux-gnu.so -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry creating /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/nmr copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/nmr/__init__.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/nmr copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/nmr/scalar_couplings.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/nmr copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/nmr/shift_wrappers.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/nmr creating /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/reporters copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/reporters/__init__.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/reporters copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/reporters/basereporter.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/reporters copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/reporters/dcdreporter.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/reporters copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/reporters/hdf5reporter.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/reporters copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/reporters/netcdfreporter.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/reporters copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/reporters/xtcreporter.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/reporters creating /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/scripts copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/scripts/__init__.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/scripts copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/scripts/mdconvert.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/scripts copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/scripts/mdinspect.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/scripts creating /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/testing copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/testing/__init__.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/testing copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/testing/docscrape.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/testing copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/testing/docstrings.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/testing copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/testing/testing.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/testing creating /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/__init__.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/contextmanagers.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/delay_import.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/rotation.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/singleton.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/six.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unitcell.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/validation.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/zipped.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils creating /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit/__init__.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit/basedimension.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit/baseunit.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit/doctests.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit/mymatrix.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit/unit.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit/constants.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit/prefix.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit/quantity.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit/standard_dimensions.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit/unit_definitions.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit/unit_math.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit/unit_operators.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/_rmsd.cpython-39-x86_64-linux-gnu.so -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/_lprmsd.cpython-39-x86_64-linux-gnu.so -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/version.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/__init__.py to __init__.cpython-39.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/io.py to io.cpython-39.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/core/__init__.py to __init__.cpython-39.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/core/element.py to element.cpython-39.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/core/residue_names.py to residue_names.cpython-39.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/core/selection.py to selection.cpython-39.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/core/topology.py to topology.cpython-39.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/core/trajectory.py to trajectory.cpython-39.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/__init__.py to __init__.cpython-39.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/amberrst.py to amberrst.cpython-39.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/arc.py to arc.cpython-39.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/gro.py to gro.cpython-39.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/gsd.py to gsd.cpython-39.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/hdf5.py to hdf5.cpython-39.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/hoomdxml.py to hoomdxml.cpython-39.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/lammpstrj.py to lammpstrj.cpython-39.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/lh5.py to lh5.cpython-39.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/mdcrd.py to mdcrd.cpython-39.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/mol2.py to mol2.cpython-39.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/netcdf.py to netcdf.cpython-39.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/openmmxml.py to openmmxml.cpython-39.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/prmtop.py to prmtop.cpython-39.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/psf.py to psf.cpython-39.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/registry.py to registry.cpython-39.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/xyzfile.py to xyzfile.cpython-39.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/pdb/__init__.py to __init__.cpython-39.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/pdb/pdbfile.py to pdbfile.cpython-39.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/pdb/pdbstructure.py to pdbstructure.cpython-39.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry/__init__.py to __init__.cpython-39.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry/alignment.py to alignment.cpython-39.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry/angle.py to angle.cpython-39.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry/contact.py to contact.cpython-39.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry/dihedral.py to dihedral.cpython-39.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry/distance.py to distance.cpython-39.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry/dssp.py to dssp.cpython-39.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry/hbond.py to hbond.cpython-39.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry/internal.py to internal.cpython-39.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry/order.py to order.cpython-39.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry/rdf.py to rdf.cpython-39.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry/rg.py to rg.cpython-39.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry/sasa.py to sasa.cpython-39.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry/shape.py to shape.cpython-39.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry/thermodynamic_properties.py to thermodynamic_properties.cpython-39.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/nmr/__init__.py to __init__.cpython-39.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/nmr/scalar_couplings.py to scalar_couplings.cpython-39.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/nmr/shift_wrappers.py to shift_wrappers.cpython-39.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/reporters/__init__.py to __init__.cpython-39.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/reporters/basereporter.py to basereporter.cpython-39.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/reporters/dcdreporter.py to dcdreporter.cpython-39.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/reporters/hdf5reporter.py to hdf5reporter.cpython-39.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/reporters/netcdfreporter.py to netcdfreporter.cpython-39.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/reporters/xtcreporter.py to xtcreporter.cpython-39.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/scripts/__init__.py to __init__.cpython-39.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/scripts/mdconvert.py to mdconvert.cpython-39.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/scripts/mdinspect.py to mdinspect.cpython-39.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/testing/__init__.py to __init__.cpython-39.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/testing/docscrape.py to docscrape.cpython-39.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/testing/docstrings.py to docstrings.cpython-39.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/testing/testing.py to testing.cpython-39.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/__init__.py to __init__.cpython-39.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/contextmanagers.py to contextmanagers.cpython-39.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/delay_import.py to delay_import.cpython-39.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/rotation.py to rotation.cpython-39.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/singleton.py to singleton.cpython-39.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/six.py to six.cpython-39.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unitcell.py to unitcell.cpython-39.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/validation.py to validation.cpython-39.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/zipped.py to zipped.cpython-39.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit/__init__.py to __init__.cpython-39.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit/basedimension.py to basedimension.cpython-39.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit/baseunit.py to baseunit.cpython-39.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit/doctests.py to doctests.cpython-39.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit/mymatrix.py to mymatrix.cpython-39.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit/unit.py to unit.cpython-39.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit/constants.py to constants.cpython-39.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit/prefix.py to prefix.cpython-39.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit/quantity.py to quantity.cpython-39.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit/standard_dimensions.py to standard_dimensions.cpython-39.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit/unit_definitions.py to unit_definitions.cpython-39.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit/unit_math.py to unit_math.cpython-39.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit/unit_operators.py to unit_operators.cpython-39.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/version.py to version.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' adding license file 'LICENSE' writing manifest file 'mdtraj.egg-info/SOURCES.txt' Copying mdtraj.egg-info to /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj-1.9.7.egg-info Skipping SOURCES.txt running install_scripts Installing mdconvert-mdtraj script to /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/bin Installing mdinspect script to /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/bin I: pybuild base:237: /usr/bin/python3 setup.py install --root /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj Using built-in specs. COLLECT_GCC=/usr/bin/x86_64-linux-gnu-gcc COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/11/lto-wrapper OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa OFFLOAD_TARGET_DEFAULT=1 Target: x86_64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 11.2.0-19' --with-bugurl=file:///usr/share/doc/gcc-11/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-11 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --enable-cet --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/gcc-11-uiwEqG/gcc-11-11.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-11-uiwEqG/gcc-11-11.2.0/debian/tmp-gcn/usr --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=2 Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 11.2.0 (Debian 11.2.0-19) 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 /usr/lib/python3/dist-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. warnings.warn( running build running build_py copying mdtraj/version.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj running build_ext running install_lib creating /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10 creating /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages creating /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/__init__.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/io.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj creating /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/core copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/core/__init__.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/core copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/core/element.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/core copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/core/residue_names.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/core copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/core/selection.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/core copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/core/topology.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/core copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/core/trajectory.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/core creating /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/core/lib copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/core/lib/libtheobald.a -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/core/lib copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/core/lib/theobald_rmsd.h -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/core/lib copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/core/lib/center.h -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/core/lib creating /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/core/__pycache__ copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/core/__pycache__/__init__.cpython-310.pyc -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/core/__pycache__ copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/core/__pycache__/element.cpython-310.pyc -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/core/__pycache__ copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/core/__pycache__/topology.cpython-310.pyc -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/core/__pycache__ copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/core/__pycache__/residue_names.cpython-310.pyc -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/core/__pycache__ copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/core/__pycache__/selection.cpython-310.pyc -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/core/__pycache__ copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/core/__pycache__/trajectory.cpython-310.pyc -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/core/__pycache__ creating /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/formats copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/formats/__init__.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/formats copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/formats/amberrst.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/formats copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/formats/arc.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/formats copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/formats/gro.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/formats copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/formats/gsd.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/formats copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/formats/hdf5.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/formats copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/formats/hoomdxml.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/formats copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/formats/lammpstrj.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/formats copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/formats/lh5.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/formats copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/formats/mdcrd.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/formats copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/formats/mol2.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/formats copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/formats/netcdf.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/formats copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/formats/openmmxml.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/formats copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/formats/prmtop.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/formats copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/formats/psf.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/formats copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/formats/registry.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/formats copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/formats/xyzfile.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/formats creating /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/formats/pdb copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/formats/pdb/__init__.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/formats/pdb copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/formats/pdb/pdbfile.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/formats/pdb copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/formats/pdb/pdbstructure.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/formats/pdb creating /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/formats/pdb/data copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/formats/pdb/data/pdbNames.xml -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/formats/pdb/data copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/formats/pdb/data/residues.xml -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/formats/pdb/data creating /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/formats/pdb/__pycache__ copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/formats/pdb/__pycache__/__init__.cpython-310.pyc -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/formats/pdb/__pycache__ copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/formats/pdb/__pycache__/pdbfile.cpython-310.pyc -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/formats/pdb/__pycache__ copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/formats/pdb/__pycache__/pdbstructure.cpython-310.pyc -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/formats/pdb/__pycache__ copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/formats/xtc.cpython-310-x86_64-linux-gnu.so -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/formats copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/formats/trr.cpython-310-x86_64-linux-gnu.so -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/formats copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/formats/tng.cpython-310-x86_64-linux-gnu.so -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/formats copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/formats/dcd.cpython-310-x86_64-linux-gnu.so -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/formats copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/formats/binpos.cpython-310-x86_64-linux-gnu.so -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/formats copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/formats/dtr.cpython-310-x86_64-linux-gnu.so -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/formats creating /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/formats/__pycache__ copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/formats/__pycache__/__init__.cpython-310.pyc -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/formats/__pycache__ copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/formats/__pycache__/arc.cpython-310.pyc -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/formats/__pycache__ copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/formats/__pycache__/registry.cpython-310.pyc -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/formats/__pycache__ copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/formats/__pycache__/hdf5.cpython-310.pyc -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/formats/__pycache__ copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/formats/__pycache__/netcdf.cpython-310.pyc -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/formats/__pycache__ copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/formats/__pycache__/lh5.cpython-310.pyc -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/formats/__pycache__ copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/formats/__pycache__/mdcrd.cpython-310.pyc -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/formats/__pycache__ copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/formats/__pycache__/amberrst.cpython-310.pyc -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/formats/__pycache__ copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/formats/__pycache__/lammpstrj.cpython-310.pyc -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/formats/__pycache__ copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/formats/__pycache__/gro.cpython-310.pyc -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/formats/__pycache__ copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/formats/__pycache__/xyzfile.cpython-310.pyc -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/formats/__pycache__ copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/formats/__pycache__/openmmxml.cpython-310.pyc -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/formats/__pycache__ copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/formats/__pycache__/prmtop.cpython-310.pyc -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/formats/__pycache__ copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/formats/__pycache__/psf.cpython-310.pyc -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/formats/__pycache__ copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/formats/__pycache__/mol2.cpython-310.pyc -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/formats/__pycache__ copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/formats/__pycache__/hoomdxml.cpython-310.pyc -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/formats/__pycache__ copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/formats/__pycache__/gsd.cpython-310.pyc -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/formats/__pycache__ creating /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/geometry copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/geometry/__init__.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/geometry copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/geometry/alignment.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/geometry copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/geometry/angle.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/geometry copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/geometry/contact.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/geometry copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/geometry/dihedral.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/geometry copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/geometry/distance.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/geometry copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/geometry/dssp.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/geometry copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/geometry/hbond.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/geometry copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/geometry/internal.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/geometry copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/geometry/order.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/geometry copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/geometry/rdf.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/geometry copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/geometry/rg.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/geometry copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/geometry/sasa.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/geometry copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/geometry/shape.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/geometry copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/geometry/thermodynamic_properties.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/geometry copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/geometry/_geometry.cpython-310-x86_64-linux-gnu.so -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/geometry copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/geometry/drid.cpython-310-x86_64-linux-gnu.so -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/geometry copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/geometry/neighbors.cpython-310-x86_64-linux-gnu.so -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/geometry copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/geometry/neighborlist.cpython-310-x86_64-linux-gnu.so -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/geometry creating /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/geometry/__pycache__ copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/geometry/__pycache__/__init__.cpython-310.pyc -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/geometry/__pycache__ copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/geometry/__pycache__/rg.cpython-310.pyc -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/geometry/__pycache__ copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/geometry/__pycache__/angle.cpython-310.pyc -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/geometry/__pycache__ copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/geometry/__pycache__/distance.cpython-310.pyc -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/geometry/__pycache__ copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/geometry/__pycache__/dihedral.cpython-310.pyc -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/geometry/__pycache__ copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/geometry/__pycache__/hbond.cpython-310.pyc -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/geometry/__pycache__ copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/geometry/__pycache__/sasa.cpython-310.pyc -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/geometry/__pycache__ copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/geometry/__pycache__/contact.cpython-310.pyc -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/geometry/__pycache__ copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/geometry/__pycache__/dssp.cpython-310.pyc -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/geometry/__pycache__ copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/geometry/__pycache__/thermodynamic_properties.cpython-310.pyc -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/geometry/__pycache__ copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/geometry/__pycache__/rdf.cpython-310.pyc -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/geometry/__pycache__ copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/geometry/__pycache__/order.cpython-310.pyc -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/geometry/__pycache__ copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/geometry/__pycache__/shape.cpython-310.pyc -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/geometry/__pycache__ creating /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/nmr copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/nmr/__init__.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/nmr copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/nmr/scalar_couplings.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/nmr copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/nmr/shift_wrappers.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/nmr creating /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/nmr/__pycache__ copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/nmr/__pycache__/__init__.cpython-310.pyc -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/nmr/__pycache__ copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/nmr/__pycache__/shift_wrappers.cpython-310.pyc -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/nmr/__pycache__ copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/nmr/__pycache__/scalar_couplings.cpython-310.pyc -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/nmr/__pycache__ creating /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/reporters copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/reporters/__init__.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/reporters copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/reporters/basereporter.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/reporters copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/reporters/dcdreporter.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/reporters copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/reporters/hdf5reporter.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/reporters copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/reporters/netcdfreporter.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/reporters copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/reporters/xtcreporter.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/reporters creating /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/reporters/__pycache__ copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/reporters/__pycache__/__init__.cpython-310.pyc -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/reporters/__pycache__ copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/reporters/__pycache__/hdf5reporter.cpython-310.pyc -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/reporters/__pycache__ copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/reporters/__pycache__/basereporter.cpython-310.pyc -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/reporters/__pycache__ copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/reporters/__pycache__/netcdfreporter.cpython-310.pyc -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/reporters/__pycache__ copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/reporters/__pycache__/dcdreporter.cpython-310.pyc -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/reporters/__pycache__ copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/reporters/__pycache__/xtcreporter.cpython-310.pyc -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/reporters/__pycache__ creating /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/scripts copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/scripts/__init__.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/scripts copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/scripts/mdconvert.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/scripts copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/scripts/mdinspect.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/scripts creating /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/testing copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/testing/__init__.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/testing copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/testing/docscrape.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/testing copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/testing/docstrings.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/testing copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/testing/testing.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/testing creating /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/utils copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/utils/__init__.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/utils copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/utils/contextmanagers.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/utils copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/utils/delay_import.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/utils copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/utils/rotation.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/utils copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/utils/singleton.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/utils copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/utils/six.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/utils copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/utils/unitcell.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/utils copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/utils/validation.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/utils copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/utils/zipped.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/utils creating /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/utils/unit copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/utils/unit/__init__.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/utils/unit copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/utils/unit/basedimension.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/utils/unit copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/utils/unit/baseunit.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/utils/unit copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/utils/unit/doctests.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/utils/unit copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/utils/unit/mymatrix.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/utils/unit copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/utils/unit/unit.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/utils/unit copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/utils/unit/constants.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/utils/unit copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/utils/unit/prefix.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/utils/unit copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/utils/unit/quantity.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/utils/unit copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/utils/unit/standard_dimensions.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/utils/unit copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/utils/unit/unit_definitions.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/utils/unit copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/utils/unit/unit_math.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/utils/unit copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/utils/unit/unit_operators.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/utils/unit creating /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/utils/unit/__pycache__/__init__.cpython-310.pyc -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/utils/unit/__pycache__/quantity.cpython-310.pyc -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/utils/unit/__pycache__/standard_dimensions.cpython-310.pyc -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/utils/unit/__pycache__/basedimension.cpython-310.pyc -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/utils/unit/__pycache__/unit.cpython-310.pyc -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/utils/unit/__pycache__/mymatrix.cpython-310.pyc -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/utils/unit/__pycache__/baseunit.cpython-310.pyc -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/utils/unit/__pycache__/unit_definitions.cpython-310.pyc -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/utils/unit/__pycache__/unit_operators.cpython-310.pyc -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/utils/unit/__pycache__/prefix.cpython-310.pyc -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/utils/unit/__pycache__ creating /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/utils/__pycache__ copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/utils/__pycache__/__init__.cpython-310.pyc -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/utils/__pycache__ copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/utils/__pycache__/delay_import.cpython-310.pyc -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/utils/__pycache__ copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/utils/__pycache__/validation.cpython-310.pyc -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/utils/__pycache__ copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/utils/__pycache__/six.cpython-310.pyc -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/utils/__pycache__ copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/utils/__pycache__/rotation.cpython-310.pyc -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/utils/__pycache__ copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/utils/__pycache__/unitcell.cpython-310.pyc -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/utils/__pycache__ copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/utils/__pycache__/contextmanagers.cpython-310.pyc -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/utils/__pycache__ copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/utils/__pycache__/zipped.cpython-310.pyc -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/utils/__pycache__ copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/utils/__pycache__/singleton.cpython-310.pyc -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/utils/__pycache__ copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/_rmsd.cpython-310-x86_64-linux-gnu.so -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/_lprmsd.cpython-310-x86_64-linux-gnu.so -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj creating /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/__pycache__ copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/__pycache__/__init__.cpython-310.pyc -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/__pycache__ copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/__pycache__/version.cpython-310.pyc -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/__pycache__ copying /build/mdtraj-X0NYWR/mdtraj-1.9.7/.pybuild/cpython3_3.10_mdtraj/build/mdtraj/version.py -> /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/__init__.py to __init__.cpython-310.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/io.py to io.cpython-310.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/core/__init__.py to __init__.cpython-310.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/core/element.py to element.cpython-310.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/core/residue_names.py to residue_names.cpython-310.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/core/selection.py to selection.cpython-310.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/core/topology.py to topology.cpython-310.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/core/trajectory.py to trajectory.cpython-310.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/formats/__init__.py to __init__.cpython-310.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/formats/amberrst.py to amberrst.cpython-310.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/formats/arc.py to arc.cpython-310.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/formats/gro.py to gro.cpython-310.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/formats/gsd.py to gsd.cpython-310.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/formats/hdf5.py to hdf5.cpython-310.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/formats/hoomdxml.py to hoomdxml.cpython-310.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/formats/lammpstrj.py to lammpstrj.cpython-310.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/formats/lh5.py to lh5.cpython-310.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/formats/mdcrd.py to mdcrd.cpython-310.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/formats/mol2.py to mol2.cpython-310.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/formats/netcdf.py to netcdf.cpython-310.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/formats/openmmxml.py to openmmxml.cpython-310.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/formats/prmtop.py to prmtop.cpython-310.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/formats/psf.py to psf.cpython-310.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/formats/registry.py to registry.cpython-310.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/formats/xyzfile.py to xyzfile.cpython-310.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/formats/pdb/__init__.py to __init__.cpython-310.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/formats/pdb/pdbfile.py to pdbfile.cpython-310.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/formats/pdb/pdbstructure.py to pdbstructure.cpython-310.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/geometry/__init__.py to __init__.cpython-310.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/geometry/alignment.py to alignment.cpython-310.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/geometry/angle.py to angle.cpython-310.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/geometry/contact.py to contact.cpython-310.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/geometry/dihedral.py to dihedral.cpython-310.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/geometry/distance.py to distance.cpython-310.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/geometry/dssp.py to dssp.cpython-310.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/geometry/hbond.py to hbond.cpython-310.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/geometry/internal.py to internal.cpython-310.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/geometry/order.py to order.cpython-310.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/geometry/rdf.py to rdf.cpython-310.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/geometry/rg.py to rg.cpython-310.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/geometry/sasa.py to sasa.cpython-310.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/geometry/shape.py to shape.cpython-310.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/geometry/thermodynamic_properties.py to thermodynamic_properties.cpython-310.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/nmr/__init__.py to __init__.cpython-310.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/nmr/scalar_couplings.py to scalar_couplings.cpython-310.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/nmr/shift_wrappers.py to shift_wrappers.cpython-310.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/reporters/__init__.py to __init__.cpython-310.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/reporters/basereporter.py to basereporter.cpython-310.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/reporters/dcdreporter.py to dcdreporter.cpython-310.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/reporters/hdf5reporter.py to hdf5reporter.cpython-310.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/reporters/netcdfreporter.py to netcdfreporter.cpython-310.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/reporters/xtcreporter.py to xtcreporter.cpython-310.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/scripts/__init__.py to __init__.cpython-310.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/scripts/mdconvert.py to mdconvert.cpython-310.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/scripts/mdinspect.py to mdinspect.cpython-310.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/testing/__init__.py to __init__.cpython-310.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/testing/docscrape.py to docscrape.cpython-310.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/testing/docstrings.py to docstrings.cpython-310.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/testing/testing.py to testing.cpython-310.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/utils/__init__.py to __init__.cpython-310.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/utils/contextmanagers.py to contextmanagers.cpython-310.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/utils/delay_import.py to delay_import.cpython-310.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/utils/rotation.py to rotation.cpython-310.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/utils/singleton.py to singleton.cpython-310.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/utils/six.py to six.cpython-310.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/utils/unitcell.py to unitcell.cpython-310.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/utils/validation.py to validation.cpython-310.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/utils/zipped.py to zipped.cpython-310.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/utils/unit/__init__.py to __init__.cpython-310.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/utils/unit/basedimension.py to basedimension.cpython-310.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/utils/unit/baseunit.py to baseunit.cpython-310.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/utils/unit/doctests.py to doctests.cpython-310.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/utils/unit/mymatrix.py to mymatrix.cpython-310.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/utils/unit/unit.py to unit.cpython-310.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/utils/unit/constants.py to constants.cpython-310.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/utils/unit/prefix.py to prefix.cpython-310.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/utils/unit/quantity.py to quantity.cpython-310.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/utils/unit/standard_dimensions.py to standard_dimensions.cpython-310.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/utils/unit/unit_definitions.py to unit_definitions.cpython-310.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/utils/unit/unit_math.py to unit_math.cpython-310.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/utils/unit/unit_operators.py to unit_operators.cpython-310.pyc byte-compiling /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj/version.py to version.cpython-310.pyc running install_egg_info running 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 reading manifest file 'mdtraj.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' no previously-included directories found matching '__pycache__' no previously-included directories found matching '*.pyc' adding license file 'LICENSE' writing manifest file 'mdtraj.egg-info/SOURCES.txt' Copying mdtraj.egg-info to /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.10/dist-packages/mdtraj-1.9.7.egg-info Skipping SOURCES.txt running install_scripts Installing mdconvert-mdtraj script to /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/bin Installing mdinspect script to /build/mdtraj-X0NYWR/mdtraj-1.9.7/debian/python3-mdtraj/usr/bin debian/rules override_dh_install make[1]: Entering directory '/build/mdtraj-X0NYWR/mdtraj-1.9.7' dh_install dh_numpy3 make[1]: Leaving directory '/build/mdtraj-X0NYWR/mdtraj-1.9.7' dh_installdocs -i -O--buildsystem=pybuild dh_installdocs: warning: Cannot auto-detect main package for python-mdtraj-doc. If the default is wrong, please use --doc-main-package debian/rules override_dh_sphinxdoc-indep make[1]: Entering directory '/build/mdtraj-X0NYWR/mdtraj-1.9.7' dh_sphinxdoc -i dh_sphinxdoc: warning: ignoring unknown JavaScript code: debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/js/versions.js sed "s|src=\"https://img.shields.io/badge/DOI-10.1016%2Fj.bpj.2015.08.015-blue.svg\"|src=\"_static/doi-10.1016_j.bpj.2015.08.015-blue.svg\"|g" -i debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/index.html make[1]: Leaving directory '/build/mdtraj-X0NYWR/mdtraj-1.9.7' dh_installchangelogs -i -O--buildsystem=pybuild dh_installexamples -i -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 -i -O--buildsystem=pybuild dh_python3 -i -O--buildsystem=pybuild E: dh_python3 dh_python3:176: no package to act on (python3-foo or one with ${python3:Depends} in Depends) dh_installsystemduser -i -O--buildsystem=pybuild dh_perl -i -O--buildsystem=pybuild dh_link -i -O--buildsystem=pybuild dh_strip_nondeterminism -i -O--buildsystem=pybuild dh_compress -i -O--buildsystem=pybuild dh_fixperms -i -O--buildsystem=pybuild dh_missing -i -O--buildsystem=pybuild dh_installdeb -i -O--buildsystem=pybuild dh_gencontrol -i -O--buildsystem=pybuild dpkg-gencontrol: warning: package python-mdtraj-doc: substitution variable ${python3:Depends} unused, but is defined dpkg-gencontrol: warning: package python-mdtraj-doc: substitution variable ${sphinxdoc:Built-Using} unused, but is defined dh_md5sums -i -O--buildsystem=pybuild dh_builddeb -i -O--buildsystem=pybuild dpkg-deb: building package 'python-mdtraj-doc' in '../python-mdtraj-doc_1.9.7-3_all.deb'. dpkg-genbuildinfo --build=all -O../mdtraj_1.9.7-3_all.buildinfo dpkg-genchanges --build=all -O../mdtraj_1.9.7-3_all.changes dpkg-genchanges: info: binary-only arch-indep upload (source code and arch-specific packages not included) dpkg-source --after-build . dpkg-source: info: using options from mdtraj-1.9.7/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/ dpkg-buildpackage: info: binary-only upload (no source included) I: running special hook: sync-out /build/mdtraj-X0NYWR /tmp/mdtraj-1.9.7-355jgahh0 I: cleaning package lists and apt cache... I: removing tempdir /tmp/mmdebstrap.r2iyty6Saz... I: success in 1040.3449 seconds md5: python-mdtraj-doc_1.9.7-3_all.deb: OK sha1: python-mdtraj-doc_1.9.7-3_all.deb: OK sha256: python-mdtraj-doc_1.9.7-3_all.deb: OK Checksums: OK