I: pbuilder: network access will be disabled during build I: Current time: Fri May 3 03:59:44 +14 2024 I: pbuilder-time-stamp: 1714658384 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [mdtraj_1.9.9-1.dsc] I: copying [./mdtraj_1.9.9.orig.tar.gz] I: copying [./mdtraj_1.9.9-1.debian.tar.xz] I: Extracting source gpgv: Signature made Tue Jan 16 11:10:34 2024 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./mdtraj_1.9.9-1.dsc: no acceptable signature found dpkg-source: info: extracting mdtraj in mdtraj-1.9.9 dpkg-source: info: unpacking mdtraj_1.9.9.orig.tar.gz dpkg-source: info: unpacking mdtraj_1.9.9-1.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 32bit_skip_image_molecule.patch dpkg-source: info: applying test_relax_tol.patch dpkg-source: info: applying rename-mdconvert-mdtraj.patch dpkg-source: info: applying drop_notebook_in_docs.patch dpkg-source: info: applying test_increase_timeout.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/4115798/tmp/hooks/D01_modify_environment starting debug: Running on codethink04-arm64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 May 2 13:59 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/4115798/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/4115798/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") BASH_VERSION='5.2.21(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=arm64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DIRSTACK=() DISTRIBUTION=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' INVOCATION_ID=63467a24207a47e7a3205824b10d5825 LANG=C LANGUAGE=nl_BE:nl LC_ALL=C MACHTYPE=aarch64-unknown-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=4115798 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.DBNKwu1j/pbuilderrc_UHiC --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.DBNKwu1j/b2 --logfile b2/build.log mdtraj_1.9.9-1.dsc' SUDO_GID=109 SUDO_UID=104 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://192.168.101.4:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-20-cloud-arm64 #1 SMP Debian 6.1.85-1 (2024-04-11) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Apr 23 11:23 /bin -> usr/bin I: user script /srv/workspace/pbuilder/4115798/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-sequence-python3, cython3-legacy, python3-setuptools, python3-all-dev, python3-numpy, python3-scipy, python3-astunparse, python3-networkx, python3-pandas, python3-pyparsing, python3-sphinx, python3-tables, libjs-mathjax, python3-msmb-theme, python3-ipykernel, python3-jupyter-client, python3-matplotlib, python3-nbconvert, python3-nbformat, python3-numpydoc, python3-six, python3-sklearn dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19915 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-sequence-python3; however: Package dh-sequence-python3 is not installed. pbuilder-satisfydepends-dummy depends on cython3-legacy; however: Package cython3-legacy is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-all-dev; however: Package python3-all-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-numpy; however: Package python3-numpy is not installed. pbuilder-satisfydepends-dummy depends on python3-scipy; however: Package python3-scipy is not installed. pbuilder-satisfydepends-dummy depends on python3-astunparse; however: Package python3-astunparse is not installed. pbuilder-satisfydepends-dummy depends on python3-networkx; however: Package python3-networkx is not installed. pbuilder-satisfydepends-dummy depends on python3-pandas; however: Package python3-pandas is not installed. pbuilder-satisfydepends-dummy depends on python3-pyparsing; however: Package python3-pyparsing is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx; however: Package python3-sphinx is not installed. pbuilder-satisfydepends-dummy depends on python3-tables; however: Package python3-tables is not installed. pbuilder-satisfydepends-dummy depends on libjs-mathjax; however: Package libjs-mathjax is not installed. pbuilder-satisfydepends-dummy depends on python3-msmb-theme; however: Package python3-msmb-theme is not installed. pbuilder-satisfydepends-dummy depends on python3-ipykernel; however: Package python3-ipykernel is not installed. pbuilder-satisfydepends-dummy depends on python3-jupyter-client; however: Package python3-jupyter-client is not installed. pbuilder-satisfydepends-dummy depends on python3-matplotlib; however: Package python3-matplotlib is not installed. pbuilder-satisfydepends-dummy depends on python3-nbconvert; however: Package python3-nbconvert is not installed. pbuilder-satisfydepends-dummy depends on python3-nbformat; however: Package python3-nbformat is not installed. pbuilder-satisfydepends-dummy depends on python3-numpydoc; however: Package python3-numpydoc is not installed. pbuilder-satisfydepends-dummy depends on python3-six; however: Package python3-six is not installed. pbuilder-satisfydepends-dummy depends on python3-sklearn; however: Package python3-sklearn is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} fonts-mathjax{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libicu72{a} libjs-mathjax{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 32 newly installed, 0 to remove and 0 not upgraded. Need to get 26.5 MB of archives. After unpacking 123 MB will be used. The following packages have unmet dependencies: pbuilder-satisfydepends-dummy : Depends: dh-sequence-python3 which is a virtual package, provided by: - dh-python (6.20240422), but it is not installable Depends: cython3-legacy but it is not installable Depends: python3-setuptools but it is not installable Depends: python3-all-dev but it is not installable Depends: python3-numpy but it is not installable Depends: python3-scipy but it is not installable Depends: python3-astunparse but it is not installable Depends: python3-networkx but it is not installable Depends: python3-pandas but it is not installable Depends: python3-pyparsing but it is not installable Depends: python3-sphinx but it is not installable Depends: python3-tables but it is not installable Depends: python3-msmb-theme but it is not installable Depends: python3-ipykernel but it is not installable Depends: python3-jupyter-client but it is not installable Depends: python3-matplotlib but it is not installable Depends: python3-nbconvert but it is not installable Depends: python3-nbformat but it is not installable Depends: python3-numpydoc but it is not installable Depends: python3-six but it is not installable Depends: python3-sklearn but it is not installable The following actions will resolve these dependencies: Remove the following packages: 1) libdb5.3 [5.3.28+dfsg2-4+b1 (now)] 2) libssl3 [3.1.5-1 (now)] Install the following packages: 3) blt [2.5.3+dfsg-7 (testing)] 4) ca-certificates [20240203 (testing)] 5) cython3-legacy [0.29.37-2 (testing)] 6) dh-python [6.20240422 (testing)] 7) docutils-common [0.20.1+dfsg-3 (testing)] 8) fontconfig-config [2.15.0-1.1 (testing)] 9) fonts-dejavu-core [2.37-8 (testing)] 10) fonts-dejavu-mono [2.37-8 (testing)] 11) fonts-font-awesome [5.0.10+really4.7.0~dfsg-4.1 (testing)] 12) fonts-lato [2.015-1 (testing)] 13) fonts-lyx [2.4.0~RC4-1 (testing)] 14) gdb [13.2-1+b1 (testing)] 15) libaec0 [1.1.3-1 (testing)] 16) libbabeltrace1 [1.5.11-3+b6 (testing)] 17) libblis4-serial [0.9.0-1+b2 (testing)] 18) libblosc1 [1.21.5+ds-1+b1 (testing)] 19) libbrotli1 [1.1.0-2+b3 (testing)] 20) libbsd0 [0.12.2-1 (testing)] 21) libcurl3t64-gnutls [8.7.1-3 (testing)] 22) libcurl4t64 [8.7.1-3 (testing)] 23) libdb5.3t64 [5.3.28+dfsg2-7 (testing)] 24) libdebuginfod-common [0.191-1 (testing)] 25) libdebuginfod1t64 [0.191-1+b1 (testing)] 26) libdeflate0 [1.20-1 (testing)] 27) libdw1t64 [0.191-1+b1 (testing)] 28) libexpat1 [2.6.2-1 (testing)] 29) libexpat1-dev [2.6.2-1 (testing)] 30) libfontconfig1 [2.15.0-1.1 (testing)] 31) libfreetype6 [2.13.2+dfsg-1+b4 (testing)] 32) libfribidi0 [1.0.13-3+b1 (testing)] 33) libgfortran5 [14-20240330-1 (testing)] 34) libglib2.0-0t64 [2.78.4-7 (testing)] 35) libgraphite2-3 [1.3.14-2 (testing)] 36) libharfbuzz0b [8.3.0-2+b1 (testing)] 37) libhdf5-103-1 [1.10.10+repack-3+b1 (testing)] 38) libimagequant0 [2.18.0-1+b1 (testing)] 39) libjbig0 [2.1-6.1+b1 (testing)] 40) libjpeg62-turbo [1:2.1.5-3 (testing)] 41) libjs-jquery [3.6.1+dfsg+~3.5.14-1 (testing)] 42) libjs-jquery-ui [1.13.2+dfsg-1 (testing)] 43) libjs-sphinxdoc [7.2.6-6 (testing)] 44) libjs-underscore [1.13.4~dfsg+~1.11.4-3 (testing)] 45) libjson-perl [4.10000-1 (testing)] 46) liblapack3 [3.12.0-3 (testing)] 47) liblbfgsb0 [3.0+dfsg.4-1+b1 (testing)] 48) liblcms2-2 [2.14-2+b1 (testing)] 49) libldap-2.5-0 [2.5.13+dfsg-5+b3 (testing)] 50) liblerc4 [4.0.0+ds-4+b1 (testing)] 51) liblzo2-2 [2.10-2+b1 (testing)] 52) libnghttp2-14 [1.59.0-1 (testing)] 53) libnorm1t64 [1.5.9+dfsg-3.1 (testing)] 54) libopenjp2-7 [2.5.0-2+b3 (testing)] 55) libpgm-5.3-0t64 [5.3.128~dfsg-2.1 (testing)] 56) libpng16-16t64 [1.6.43-5 (testing)] 57) libproc2-0 [2:4.0.4-4 (testing)] 58) libpsl5t64 [0.21.2-1.1 (testing)] 59) libpython3-all-dev [3.11.8-1 (testing)] 60) libpython3-dev [3.11.8-1 (testing)] 61) libpython3-stdlib [3.11.8-1 (testing)] 62) libpython3.11-dev [3.11.9-1 (testing)] 63) libpython3.11-minimal [3.11.9-1 (testing)] 64) libpython3.11-stdlib [3.11.9-1 (testing)] 65) libpython3.11t64 [3.11.9-1 (testing)] 66) libpython3.12-dev [3.12.3-1 (testing)] 67) libpython3.12-minimal [3.12.3-1 (testing)] 68) libpython3.12-stdlib [3.12.3-1 (testing)] 69) libpython3.12t64 [3.12.3-1 (testing)] 70) libqhull-r8.0 [2020.2-6+b1 (testing)] 71) libraqm0 [0.10.1-1+b1 (testing)] 72) libreadline8t64 [8.2-4 (testing)] 73) librtmp1 [2.4+20151223.gitfa8646d.1-2+b4 (testing)] 74) libsasl2-2 [2.1.28+dfsg1-4+b1 (testing)] 75) libsasl2-modules-db [2.1.28+dfsg1-4+b1 (testing)] 76) libsharpyuv0 [1.3.2-0.4+b1 (testing)] 77) libsnappy1v5 [1.1.10-1+b1 (testing)] 78) libsodium23 [1.0.18-1+b1 (testing)] 79) libsource-highlight-common [3.1.9-4.3 (testing)] 80) libsource-highlight4t64 [3.1.9-4.3 (testing)] 81) libssh2-1t64 [1.11.0-4.1+b2 (testing)] 82) libssl3t64 [3.2.1-3 (testing)] 83) libsz2 [1.1.3-1 (testing)] 84) libtcl8.6 [8.6.14+dfsg-1 (testing)] 85) libtiff6 [4.5.1+git230720-4 (testing)] 86) libtk8.6 [8.6.14-1 (testing)] 87) libwebp7 [1.3.2-0.4+b1 (testing)] 88) libwebpdemux2 [1.3.2-0.4+b1 (testing)] 89) libwebpmux3 [1.3.2-0.4+b1 (testing)] 90) libx11-6 [2:1.8.7-1+b1 (testing)] 91) libx11-data [2:1.8.7-1 (testing)] 92) libxau6 [1:1.0.9-1+b1 (testing)] 93) libxcb1 [1.15-1 (testing)] 94) libxdmcp6 [1:1.1.2-3+b1 (testing)] 95) libxext6 [2:1.3.4-1+b1 (testing)] 96) libxft2 [2.3.6-1+b1 (testing)] 97) libxrender1 [1:0.9.10-1.1+b1 (testing)] 98) libxslt1.1 [1.1.35-1+b1 (testing)] 99) libxss1 [1:1.2.3-1+b1 (testing)] 100) libzmq5 [4.3.5-1+b2 (testing)] 101) media-types [10.1.0 (testing)] 102) netbase [6.4 (testing)] 103) openssl [3.2.1-3 (testing)] 104) procps [2:4.0.4-4 (testing)] 105) python-babel-localedata [2.14.0-1 (testing)] 106) python-matplotlib-data [3.6.3-1 (testing)] 107) python-tables-data [3.7.0-10 (testing)] 108) python-tinycss2-common [1.2.1-2 (testing)] 109) python3 [3.11.8-1 (testing)] 110) python3-alabaster [0.7.12-1 (testing)] 111) python3-all [3.11.8-1 (testing)] 112) python3-all-dev [3.11.8-1 (testing)] 113) python3-appdirs [1.4.4-4 (testing)] 114) python3-asttokens [2.4.1-1 (testing)] 115) python3-astunparse [1.6.3-2 (testing)] 116) python3-attr [23.2.0-2 (testing)] 117) python3-babel [2.14.0-1 (testing)] 118) python3-bleach [6.1.0-2 (testing)] 119) python3-brotli [1.1.0-2+b3 (testing)] 120) python3-bs4 [4.12.3-1 (testing)] 121) python3-bytecode [0.15.1-3 (testing)] 122) python3-certifi [2023.11.17-1 (testing)] 123) python3-cffi-backend [1.16.0-2+b2 (testing)] 124) python3-chardet [5.2.0+dfsg-1 (testing)] 125) python3-charset-normalizer [3.3.2-1 (testing)] 126) python3-comm [0.2.1-1 (testing)] 127) python3-contourpy [1.0.7-3 (testing)] 128) python3-coverage [7.2.7+dfsg1-1+b1 (testing)] 129) python3-cycler [0.12.1-1 (testing)] 130) python3-dateutil [2.9.0-2 (testing)] 131) python3-debugpy [1.8.0+ds-4 (testing)] 132) python3-decorator [5.1.1-5 (testing)] 133) python3-defusedxml [0.7.1-2 (testing)] 134) python3-dev [3.11.8-1 (testing)] 135) python3-distutils [3.12.3-1 (testing)] 136) python3-docutils [0.20.1+dfsg-3 (testing)] 137) python3-entrypoints [0.4-2 (testing)] 138) python3-executing [2.0.1-0.1 (testing)] 139) python3-fastjsonschema [2.19.1-1 (testing)] 140) python3-fonttools [4.46.0-1 (testing)] 141) python3-fs [2.4.16-4 (testing)] 142) python3-hatch-vcs [0.4.0-1 (testing)] 143) python3-hatchling [1.24.2-1 (testing)] 144) python3-html5lib [1.1-6 (testing)] 145) python3-idna [3.6-2 (testing)] 146) python3-imagesize [1.4.1-1 (testing)] 147) python3-ipykernel [6.29.3-1 (testing)] 148) python3-ipython [8.20.0-1 (testing)] 149) python3-jedi [0.19.1+ds1-1 (testing)] 150) python3-jinja2 [3.1.3-1 (testing)] 151) python3-joblib [1.3.2-2 (testing)] 152) python3-jsonschema [4.19.2-2 (testing)] 153) python3-jsonschema-specifications [2023.12.1-1 (testing)] 154) python3-jupyter-client [7.4.9-2 (testing)] 155) python3-jupyter-core [5.3.2-1 (testing)] 156) python3-jupyterlab-pygments [0.2.2-3 (testing)] 157) python3-kiwisolver [1.4.5-1 (testing)] 158) python3-lib2to3 [3.12.3-1 (testing)] 159) python3-lxml [5.1.0-1 (testing)] 160) python3-lxml-html-clean [0.1.1-1 (testing)] 161) python3-lz4 [4.0.2+dfsg-1+b3 (testing)] 162) python3-markupsafe [2.1.5-1 (testing)] 163) python3-matplotlib [3.6.3-1+b2 (testing)] 164) python3-matplotlib-inline [0.1.6-2 (testing)] 165) python3-minimal [3.11.8-1 (testing)] 166) python3-mpmath [1.3.0-1 (testing)] 167) python3-msmb-theme [1.2.0-4 (testing)] 168) python3-nbclient [0.8.0-1 (testing)] 169) python3-nbconvert [6.5.3-5 (testing)] 170) python3-nbformat [5.9.1-1 (testing)] 171) python3-nest-asyncio [1.5.4-1 (testing)] 172) python3-networkx [2.8.8-2 (testing)] 173) python3-numexpr [2.9.0-1 (testing)] 174) python3-numpy [1:1.24.2-2 (testing)] 175) python3-numpydoc [1.6.0-2 (testing)] 176) python3-packaging [24.0-1 (testing)] 177) python3-pandas [2.1.4+dfsg-5 (testing)] 178) python3-pandas-lib [2.1.4+dfsg-5 (testing)] 179) python3-pandocfilters [1.5.1-1 (testing)] 180) python3-parso [0.8.3-1 (testing)] 181) python3-pathspec [0.12.1-1 (testing)] 182) python3-pexpect [4.9-2 (testing)] 183) python3-pil [10.3.0-2 (testing)] 184) python3-pil.imagetk [10.3.0-2 (testing)] 185) python3-pkg-resources [68.1.2-2 (testing)] 186) python3-platformdirs [4.2.1-1 (testing)] 187) python3-pluggy [1.5.0-1 (testing)] 188) python3-prompt-toolkit [3.0.43-1 (testing)] 189) python3-psutil [5.9.8-2 (testing)] 190) python3-ptyprocess [0.7.0-5 (testing)] 191) python3-pure-eval [0.2.2-2 (testing)] 192) python3-py [1.11.0-2 (testing)] 193) python3-pydevd [2.10.0+ds-10 (testing)] 194) python3-pygments [2.17.2+dfsg-1 (testing)] 195) python3-pyparsing [3.1.2-1 (testing)] 196) python3-referencing [0.31.0-1 (testing)] 197) python3-requests [2.31.0+dfsg-1 (testing)] 198) python3-roman [3.3-3 (testing)] 199) python3-rpds-py [0.12.0-3 (testing)] 200) python3-scipy [1.11.4-6 (testing)] 201) python3-setuptools [68.1.2-2 (testing)] 202) python3-setuptools-scm [8.0.4-2 (testing)] 203) python3-six [1.16.0-6 (testing)] 204) python3-sklearn [1.4.1.post1+dfsg-1 (testing)] 205) python3-sklearn-lib [1.4.1.post1+dfsg-1 (testing)] 206) python3-snowballstemmer [2.2.0-4 (testing)] 207) python3-soupsieve [2.5-1 (testing)] 208) python3-sphinx [7.2.6-6 (testing)] 209) python3-sphinx-rtd-theme [2.0.0+dfsg-1 (testing)] 210) python3-sphinxcontrib.jquery [4.1-5 (testing)] 211) python3-stack-data [0.6.3-1 (testing)] 212) python3-sympy [1.12-7 (testing)] 213) python3-tables [3.7.0-10 (testing)] 214) python3-tables-lib [3.7.0-10+b1 (testing)] 215) python3-tabulate [0.8.10-1 (testing)] 216) python3-threadpoolctl [3.1.0-1 (testing)] 217) python3-tinycss2 [1.2.1-2 (testing)] 218) python3-tk [3.12.3-1 (testing)] 219) python3-tornado [6.4.0-1 (testing)] 220) python3-traitlets [5.5.0-2 (testing)] 221) python3-trove-classifiers [2024.1.31-1 (testing)] 222) python3-typeshed [0.0~git20231111.6764465-3 (testing)] 223) python3-typing-extensions [4.10.0-1 (testing)] 224) python3-tz [2024.1-2 (testing)] 225) python3-ufolib2 [0.16.0+dfsg1-1 (testing)] 226) python3-urllib3 [1.26.18-2 (testing)] 227) python3-wcwidth [0.2.13+dfsg1-1 (testing)] 228) python3-webencodings [0.5.1-5 (testing)] 229) python3-zmq [24.0.1-5+b1 (testing)] 230) python3-zombie-imp [0.0.2-2 (testing)] 231) python3.11 [3.11.9-1 (testing)] 232) python3.11-dev [3.11.9-1 (testing)] 233) python3.11-minimal [3.11.9-1 (testing)] 234) python3.12 [3.12.3-1 (testing)] 235) python3.12-dev [3.12.3-1 (testing)] 236) python3.12-minimal [3.12.3-1 (testing)] 237) readline-common [8.2-4 (testing)] 238) sgml-base [1.31 (testing)] 239) sphinx-common [7.2.6-6 (testing)] 240) sphinx-rtd-theme-common [2.0.0+dfsg-1 (testing)] 241) tk8.6-blt2.5 [2.5.3+dfsg-7 (testing)] 242) tzdata [2024a-3 (testing)] 243) ucf [3.0043+nmu1 (testing)] 244) unicode-data [15.1.0-1 (testing)] 245) x11-common [1:7.7+23 (testing)] 246) xml-core [0.19 (testing)] 247) zlib1g-dev [1:1.3.dfsg-3.1 (testing)] The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} blt{a} bsdextrautils{a} ca-certificates{a} cython3-legacy{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} docutils-common{a} dwz{a} file{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} fonts-font-awesome{a} fonts-lato{a} fonts-lyx{a} fonts-mathjax{a} gdb{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libaec0{a} libarchive-zip-perl{a} libbabeltrace1{a} libblis4-serial{a} libblosc1{a} libbrotli1{a} libbsd0{a} libcurl3t64-gnutls{a} libcurl4t64{a} libdb5.3t64{a} libdebhelper-perl{a} libdebuginfod-common{a} libdebuginfod1t64{a} libdeflate0{a} libdw1t64{a} libelf1t64{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgfortran5{a} libglib2.0-0t64{a} libgraphite2-3{a} libharfbuzz0b{a} libhdf5-103-1{a} libicu72{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-jquery-ui{a} libjs-mathjax{a} libjs-sphinxdoc{a} libjs-underscore{a} libjson-perl{a} liblapack3{a} liblbfgsb0{a} liblcms2-2{a} libldap-2.5-0{a} liblerc4{a} liblzo2-2{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnorm1t64{a} libopenjp2-7{a} libpgm-5.3-0t64{a} libpipeline1{a} libpng16-16t64{a} libproc2-0{a} libpsl5t64{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.11-dev{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libpython3.11t64{a} libpython3.12-dev{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libpython3.12t64{a} libqhull-r8.0{a} libraqm0{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsharpyuv0{a} libsnappy1v5{a} libsodium23{a} libsource-highlight-common{a} libsource-highlight4t64{a} libssh2-1t64{a} libssl3t64{a} libsub-override-perl{a} libsz2{a} libtcl8.6{a} libtiff6{a} libtk8.6{a} libtool{a} libuchardet0{a} libwebp7{a} libwebpdemux2{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxft2{a} libxml2{a} libxrender1{a} libxslt1.1{a} libxss1{a} libzmq5{a} m4{a} man-db{a} media-types{a} netbase{a} openssl{a} po-debconf{a} procps{a} python-babel-localedata{a} python-matplotlib-data{a} python-tables-data{a} python-tinycss2-common{a} python3{a} python3-alabaster{a} python3-all{a} python3-all-dev{a} python3-appdirs{a} python3-asttokens{a} python3-astunparse{a} python3-attr{a} python3-babel{a} python3-bleach{a} python3-brotli{a} python3-bs4{a} python3-bytecode{a} python3-certifi{a} python3-cffi-backend{a} python3-chardet{a} python3-charset-normalizer{a} python3-comm{a} python3-contourpy{a} python3-coverage{a} python3-cycler{a} python3-dateutil{a} python3-debugpy{a} python3-decorator{a} python3-defusedxml{a} python3-dev{a} python3-distutils{a} python3-docutils{a} python3-entrypoints{a} python3-executing{a} python3-fastjsonschema{a} python3-fonttools{a} python3-fs{a} python3-hatch-vcs{a} python3-hatchling{a} python3-html5lib{a} python3-idna{a} python3-imagesize{a} python3-ipykernel{a} python3-ipython{a} python3-jedi{a} python3-jinja2{a} python3-joblib{a} python3-jsonschema{a} python3-jsonschema-specifications{a} python3-jupyter-client{a} python3-jupyter-core{a} python3-jupyterlab-pygments{a} python3-kiwisolver{a} python3-lib2to3{a} python3-lxml{a} python3-lxml-html-clean{a} python3-lz4{a} python3-markupsafe{a} python3-matplotlib{a} python3-matplotlib-inline{a} python3-minimal{a} python3-mpmath{a} python3-msmb-theme{a} python3-nbclient{a} python3-nbconvert{a} python3-nbformat{a} python3-nest-asyncio{a} python3-networkx{a} python3-numexpr{a} python3-numpy{a} python3-numpydoc{a} python3-packaging{a} python3-pandas{a} python3-pandas-lib{a} python3-pandocfilters{a} python3-parso{a} python3-pathspec{a} python3-pexpect{a} python3-pil{a} python3-pil.imagetk{a} python3-pkg-resources{a} python3-platformdirs{a} python3-pluggy{a} python3-prompt-toolkit{a} python3-psutil{a} python3-ptyprocess{a} python3-pure-eval{a} python3-py{a} python3-pydevd{a} python3-pygments{a} python3-pyparsing{a} python3-referencing{a} python3-requests{a} python3-roman{a} python3-rpds-py{a} python3-scipy{a} python3-setuptools{a} python3-setuptools-scm{a} python3-six{a} python3-sklearn{a} python3-sklearn-lib{a} python3-snowballstemmer{a} python3-soupsieve{a} python3-sphinx{a} python3-sphinx-rtd-theme{a} python3-sphinxcontrib.jquery{a} python3-stack-data{a} python3-sympy{a} python3-tables{a} python3-tables-lib{a} python3-tabulate{a} python3-threadpoolctl{a} python3-tinycss2{a} python3-tk{a} python3-tornado{a} python3-traitlets{a} python3-trove-classifiers{a} python3-typeshed{a} python3-typing-extensions{a} python3-tz{a} python3-ufolib2{a} python3-urllib3{a} python3-wcwidth{a} python3-webencodings{a} python3-zmq{a} python3-zombie-imp{a} python3.11{a} python3.11-dev{a} python3.11-minimal{a} python3.12{a} python3.12-dev{a} python3.12-minimal{a} readline-common{a} sensible-utils{a} sgml-base{a} sphinx-common{a} sphinx-rtd-theme-common{a} tk8.6-blt2.5{a} tzdata{a} ucf{a} unicode-data{a} x11-common{a} xml-core{a} zlib1g-dev{a} The following packages will be REMOVED: libdb5.3{a} libssl3{a} The following packages are RECOMMENDED but will NOT be installed: curl isympy-common javascript-common libarchive-cpio-perl libc6-dbg libglib2.0-data libjson-xs-perl libldap-common libltdl-dev libmail-sendmail-perl libpaper-utils libsasl2-modules lynx pandoc psmisc publicsuffix python3-bottleneck python3-cssselect python3-gdal python3-json-pointer python3-odf python3-olefile python3-openpyxl python3-pydot python3-pygraphviz python3-pytest python3-rfc3987 python3-simplejson python3-uritemplate python3-webcolors python3-yaml shared-mime-info wget xdg-user-dirs 0 packages upgraded, 277 newly installed, 2 to remove and 0 not upgraded. Need to get 178 MB of archives. After unpacking 851 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 libdb5.3t64 arm64 5.3.28+dfsg2-7 [625 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 libssl3t64 arm64 3.2.1-3 [2537 kB] Get: 3 http://deb.debian.org/debian trixie/main arm64 fonts-lato all 2.015-1 [2780 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.22 [22.4 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 ucf all 3.0043+nmu1 [55.2 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 libdebuginfod-common all 0.191-1 [22.9 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 libpython3.11-minimal arm64 3.11.9-1 [813 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 libexpat1 arm64 2.6.2-1 [88.7 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 python3.11-minimal arm64 3.11.9-1 [1767 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 python3-minimal arm64 3.11.8-1 [26.3 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 media-types all 10.1.0 [26.9 kB] Get: 12 http://deb.debian.org/debian trixie/main arm64 netbase all 6.4 [12.8 kB] Get: 13 http://deb.debian.org/debian trixie/main arm64 tzdata all 2024a-3 [255 kB] Get: 14 http://deb.debian.org/debian trixie/main arm64 readline-common all 8.2-4 [69.3 kB] Get: 15 http://deb.debian.org/debian trixie/main arm64 libreadline8t64 arm64 8.2-4 [157 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 libpython3.11-stdlib arm64 3.11.9-1 [1775 kB] Get: 17 http://deb.debian.org/debian trixie/main arm64 python3.11 arm64 3.11.9-1 [602 kB] Get: 18 http://deb.debian.org/debian trixie/main arm64 libpython3-stdlib arm64 3.11.8-1 [9332 B] Get: 19 http://deb.debian.org/debian trixie/main arm64 python3 arm64 3.11.8-1 [27.4 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 libpython3.12-minimal arm64 3.12.3-1 [802 kB] Get: 21 http://deb.debian.org/debian trixie/main arm64 python3.12-minimal arm64 3.12.3-1 [1931 kB] Get: 22 http://deb.debian.org/debian trixie/main arm64 sgml-base all 1.31 [15.4 kB] Get: 23 http://deb.debian.org/debian trixie/main arm64 libproc2-0 arm64 2:4.0.4-4 [61.7 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 procps arm64 2:4.0.4-4 [869 kB] Get: 25 http://deb.debian.org/debian trixie/main arm64 openssl arm64 3.2.1-3 [1324 kB] Get: 26 http://deb.debian.org/debian trixie/main arm64 ca-certificates all 20240203 [158 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-3 [314 kB] Get: 28 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.45-3 [100 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-3 [43.0 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.21-14+b1 [160 kB] Get: 31 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b1 [69.0 kB] Get: 32 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-3+b1 [1126 kB] Get: 33 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.40-8 [93.0 kB] Get: 34 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.7-2 [36.5 kB] Get: 35 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.12.0-3 [1385 kB] Get: 36 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 37 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.71-3 [332 kB] Get: 38 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 39 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 40 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.21-14 [496 kB] Get: 41 http://deb.debian.org/debian trixie/main arm64 libtcl8.6 arm64 8.6.14+dfsg-1 [975 kB] Get: 42 http://deb.debian.org/debian trixie/main arm64 libbrotli1 arm64 1.1.0-2+b3 [295 kB] Get: 43 http://deb.debian.org/debian trixie/main arm64 libpng16-16t64 arm64 1.6.43-5 [272 kB] Get: 44 http://deb.debian.org/debian trixie/main arm64 libfreetype6 arm64 2.13.2+dfsg-1+b4 [408 kB] Get: 45 http://deb.debian.org/debian trixie/main arm64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 46 http://deb.debian.org/debian trixie/main arm64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 47 http://deb.debian.org/debian trixie/main arm64 fontconfig-config arm64 2.15.0-1.1 [317 kB] Get: 48 http://deb.debian.org/debian trixie/main arm64 libfontconfig1 arm64 2.15.0-1.1 [385 kB] Get: 49 http://deb.debian.org/debian trixie/main arm64 libxau6 arm64 1:1.0.9-1+b1 [18.1 kB] Get: 50 http://deb.debian.org/debian trixie/main arm64 libbsd0 arm64 0.12.2-1 [129 kB] Get: 51 http://deb.debian.org/debian trixie/main arm64 libxdmcp6 arm64 1:1.1.2-3+b1 [24.3 kB] Get: 52 http://deb.debian.org/debian trixie/main arm64 libxcb1 arm64 1.15-1 [143 kB] Get: 53 http://deb.debian.org/debian trixie/main arm64 libx11-data all 2:1.8.7-1 [328 kB] Get: 54 http://deb.debian.org/debian trixie/main arm64 libx11-6 arm64 2:1.8.7-1+b1 [775 kB] Get: 55 http://deb.debian.org/debian trixie/main arm64 libxrender1 arm64 1:0.9.10-1.1+b1 [27.0 kB] Get: 56 http://deb.debian.org/debian trixie/main arm64 libxft2 arm64 2.3.6-1+b1 [51.0 kB] Get: 57 http://deb.debian.org/debian trixie/main arm64 libxext6 arm64 2:1.3.4-1+b1 [51.7 kB] Get: 58 http://deb.debian.org/debian trixie/main arm64 x11-common all 1:7.7+23 [252 kB] Get: 59 http://deb.debian.org/debian trixie/main arm64 libxss1 arm64 1:1.2.3-1+b1 [17.0 kB] Get: 60 http://deb.debian.org/debian trixie/main arm64 libtk8.6 arm64 8.6.14-1 [732 kB] Get: 61 http://deb.debian.org/debian trixie/main arm64 tk8.6-blt2.5 arm64 2.5.3+dfsg-7 [533 kB] Get: 62 http://deb.debian.org/debian trixie/main arm64 blt arm64 2.5.3+dfsg-7 [6024 B] Get: 63 http://deb.debian.org/debian trixie/main arm64 python3-zombie-imp all 0.0.2-2 [11.7 kB] Get: 64 http://deb.debian.org/debian trixie/main arm64 cython3-legacy arm64 0.29.37-2 [2672 kB] Get: 65 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 66 http://deb.debian.org/debian trixie/main arm64 libtool all 2.4.7-7 [517 kB] Get: 67 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 68 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 69 http://deb.debian.org/debian trixie/main arm64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 70 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 71 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 72 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.191-1+b1 [187 kB] Get: 73 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 74 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-4+b1 [9224 kB] Get: 75 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.9.14+dfsg-1.3+b3 [624 kB] Get: 76 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.21-14+b1 [1249 kB] Get: 77 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 78 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 79 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.15.3 [901 kB] Get: 80 http://deb.debian.org/debian trixie/main arm64 python3-pkg-resources all 68.1.2-2 [241 kB] Get: 81 http://deb.debian.org/debian trixie/main arm64 python3-lib2to3 all 3.12.3-1 [77.6 kB] Get: 82 http://deb.debian.org/debian trixie/main arm64 python3-distutils all 3.12.3-1 [131 kB] Get: 83 http://deb.debian.org/debian trixie/main arm64 python3-setuptools all 68.1.2-2 [468 kB] Get: 84 http://deb.debian.org/debian trixie/main arm64 dh-python all 6.20240422 [107 kB] Get: 85 http://deb.debian.org/debian trixie/main arm64 xml-core all 0.19 [20.1 kB] Get: 86 http://deb.debian.org/debian trixie/main arm64 docutils-common all 0.20.1+dfsg-3 [128 kB] Get: 87 http://deb.debian.org/debian trixie/main arm64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [517 kB] Get: 88 http://deb.debian.org/debian trixie/main arm64 fonts-lyx all 2.4.0~RC4-1 [189 kB] Get: 89 http://deb.debian.org/debian trixie/main arm64 fonts-mathjax all 2.7.9+dfsg-1 [2210 kB] Get: 90 http://deb.debian.org/debian trixie/main arm64 libdw1t64 arm64 0.191-1+b1 [230 kB] Get: 91 http://deb.debian.org/debian trixie/main arm64 libglib2.0-0t64 arm64 2.78.4-7 [1364 kB] Get: 92 http://deb.debian.org/debian trixie/main arm64 libbabeltrace1 arm64 1.5.11-3+b6 [163 kB] Get: 93 http://deb.debian.org/debian trixie/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-4+b1 [20.2 kB] Get: 94 http://deb.debian.org/debian trixie/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-4+b1 [55.5 kB] Get: 95 http://deb.debian.org/debian trixie/main arm64 libldap-2.5-0 arm64 2.5.13+dfsg-5+b3 [172 kB] Get: 96 http://deb.debian.org/debian trixie/main arm64 libnghttp2-14 arm64 1.59.0-1 [70.2 kB] Get: 97 http://deb.debian.org/debian trixie/main arm64 libpsl5t64 arm64 0.21.2-1.1 [56.8 kB] Get: 98 http://deb.debian.org/debian trixie/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b4 [56.7 kB] Get: 99 http://deb.debian.org/debian trixie/main arm64 libssh2-1t64 arm64 1.11.0-4.1+b2 [207 kB] Get: 100 http://deb.debian.org/debian trixie/main arm64 libcurl3t64-gnutls arm64 8.7.1-3 [405 kB] Get: 101 http://deb.debian.org/debian trixie/main arm64 libdebuginfod1t64 arm64 0.191-1+b1 [27.5 kB] Get: 102 http://deb.debian.org/debian trixie/main arm64 libpython3.11t64 arm64 3.11.9-1 [1814 kB] Get: 103 http://deb.debian.org/debian trixie/main arm64 libsource-highlight-common all 3.1.9-4.3 [77.5 kB] Get: 104 http://deb.debian.org/debian trixie/main arm64 libsource-highlight4t64 arm64 3.1.9-4.3 [289 kB] Get: 105 http://deb.debian.org/debian trixie/main arm64 gdb arm64 13.2-1+b1 [3675 kB] Get: 106 http://deb.debian.org/debian trixie/main arm64 libaec0 arm64 1.1.3-1 [22.1 kB] Get: 107 http://deb.debian.org/debian trixie/main arm64 libblis4-serial arm64 0.9.0-1+b2 [791 kB] Get: 108 http://deb.debian.org/debian trixie/main arm64 libsnappy1v5 arm64 1.1.10-1+b1 [27.1 kB] Get: 109 http://deb.debian.org/debian trixie/main arm64 libblosc1 arm64 1.21.5+ds-1+b1 [39.0 kB] Get: 110 http://deb.debian.org/debian trixie/main arm64 libcurl4t64 arm64 8.7.1-3 [412 kB] Get: 111 http://deb.debian.org/debian trixie/main arm64 libdeflate0 arm64 1.20-1 [41.5 kB] Get: 112 http://deb.debian.org/debian trixie/main arm64 libexpat1-dev arm64 2.6.2-1 [278 kB] Get: 113 http://deb.debian.org/debian trixie/main arm64 libfribidi0 arm64 1.0.13-3+b1 [71.3 kB] Get: 114 http://deb.debian.org/debian trixie/main arm64 libgfortran5 arm64 14-20240330-1 [361 kB] Get: 115 http://deb.debian.org/debian trixie/main arm64 libgraphite2-3 arm64 1.3.14-2 [69.2 kB] Get: 116 http://deb.debian.org/debian trixie/main arm64 libharfbuzz0b arm64 8.3.0-2+b1 [2178 kB] Get: 117 http://deb.debian.org/debian trixie/main arm64 libsz2 arm64 1.1.3-1 [7664 B] Get: 118 http://deb.debian.org/debian trixie/main arm64 libhdf5-103-1 arm64 1.10.10+repack-3+b1 [1036 kB] Get: 119 http://deb.debian.org/debian trixie/main arm64 libimagequant0 arm64 2.18.0-1+b1 [34.6 kB] Get: 120 http://deb.debian.org/debian trixie/main arm64 libjbig0 arm64 2.1-6.1+b1 [30.4 kB] Get: 121 http://deb.debian.org/debian trixie/main arm64 libjpeg62-turbo arm64 1:2.1.5-3 [172 kB] Get: 122 http://deb.debian.org/debian trixie/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 123 http://deb.debian.org/debian trixie/main arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 124 http://deb.debian.org/debian trixie/main arm64 libjs-mathjax all 2.7.9+dfsg-1 [5667 kB] Get: 125 http://deb.debian.org/debian trixie/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 126 http://deb.debian.org/debian trixie/main arm64 libjs-sphinxdoc all 7.2.6-6 [150 kB] Get: 127 http://deb.debian.org/debian trixie/main arm64 libjson-perl all 4.10000-1 [87.5 kB] Get: 128 http://deb.debian.org/debian trixie/main arm64 liblapack3 arm64 3.12.0-3 [1757 kB] Get: 129 http://deb.debian.org/debian trixie/main arm64 liblbfgsb0 arm64 3.0+dfsg.4-1+b1 [25.0 kB] Get: 130 http://deb.debian.org/debian trixie/main arm64 liblcms2-2 arm64 2.14-2+b1 [144 kB] Get: 131 http://deb.debian.org/debian trixie/main arm64 liblerc4 arm64 4.0.0+ds-4+b1 [142 kB] Get: 132 http://deb.debian.org/debian trixie/main arm64 liblzo2-2 arm64 2.10-2+b1 [49.2 kB] Get: 133 http://deb.debian.org/debian trixie/main arm64 libnorm1t64 arm64 1.5.9+dfsg-3.1 [204 kB] Get: 134 http://deb.debian.org/debian trixie/main arm64 libopenjp2-7 arm64 2.5.0-2+b3 [177 kB] Get: 135 http://deb.debian.org/debian trixie/main arm64 libpgm-5.3-0t64 arm64 5.3.128~dfsg-2.1 [151 kB] Get: 136 http://deb.debian.org/debian trixie/main arm64 zlib1g-dev arm64 1:1.3.dfsg-3.1 [915 kB] Get: 137 http://deb.debian.org/debian trixie/main arm64 libpython3.11-dev arm64 3.11.9-1 [4358 kB] Get: 138 http://deb.debian.org/debian trixie/main arm64 libpython3-dev arm64 3.11.8-1 [9564 B] Get: 139 http://deb.debian.org/debian trixie/main arm64 libpython3.12-stdlib arm64 3.12.3-1 [1889 kB] Get: 140 http://deb.debian.org/debian trixie/main arm64 libpython3.12t64 arm64 3.12.3-1 [1948 kB] Get: 141 http://deb.debian.org/debian trixie/main arm64 libpython3.12-dev arm64 3.12.3-1 [4745 kB] Get: 142 http://deb.debian.org/debian trixie/main arm64 libpython3-all-dev arm64 3.11.8-1 [1072 B] Get: 143 http://deb.debian.org/debian trixie/main arm64 libqhull-r8.0 arm64 2020.2-6+b1 [226 kB] Get: 144 http://deb.debian.org/debian trixie/main arm64 libraqm0 arm64 0.10.1-1+b1 [13.7 kB] Get: 145 http://deb.debian.org/debian trixie/main arm64 libsharpyuv0 arm64 1.3.2-0.4+b1 [107 kB] Get: 146 http://deb.debian.org/debian trixie/main arm64 libsodium23 arm64 1.0.18-1+b1 [118 kB] Get: 147 http://deb.debian.org/debian trixie/main arm64 libwebp7 arm64 1.3.2-0.4+b1 [263 kB] Get: 148 http://deb.debian.org/debian trixie/main arm64 libtiff6 arm64 4.5.1+git230720-4 [307 kB] Get: 149 http://deb.debian.org/debian trixie/main arm64 libwebpdemux2 arm64 1.3.2-0.4+b1 [107 kB] Get: 150 http://deb.debian.org/debian trixie/main arm64 libwebpmux3 arm64 1.3.2-0.4+b1 [119 kB] Get: 151 http://deb.debian.org/debian trixie/main arm64 libxslt1.1 arm64 1.1.35-1+b1 [221 kB] Get: 152 http://deb.debian.org/debian trixie/main arm64 libzmq5 arm64 4.3.5-1+b2 [251 kB] Get: 153 http://deb.debian.org/debian trixie/main arm64 python-babel-localedata all 2.14.0-1 [5701 kB] Get: 154 http://deb.debian.org/debian trixie/main arm64 python-matplotlib-data all 3.6.3-1 [2744 kB] Get: 155 http://deb.debian.org/debian trixie/main arm64 python-tables-data all 3.7.0-10 [47.6 kB] Get: 156 http://deb.debian.org/debian trixie/main arm64 python-tinycss2-common all 1.2.1-2 [31.5 kB] Get: 157 http://deb.debian.org/debian trixie/main arm64 python3-alabaster all 0.7.12-1 [20.8 kB] Get: 158 http://deb.debian.org/debian trixie/main arm64 python3.12 arm64 3.12.3-1 [659 kB] Get: 159 http://deb.debian.org/debian trixie/main arm64 python3-all arm64 3.11.8-1 [1056 B] Get: 160 http://deb.debian.org/debian trixie/main arm64 python3.11-dev arm64 3.11.9-1 [501 kB] Get: 161 http://deb.debian.org/debian trixie/main arm64 python3-dev arm64 3.11.8-1 [26.1 kB] Get: 162 http://deb.debian.org/debian trixie/main arm64 python3.12-dev arm64 3.12.3-1 [499 kB] Get: 163 http://deb.debian.org/debian trixie/main arm64 python3-all-dev arm64 3.11.8-1 [1072 B] Get: 164 http://deb.debian.org/debian trixie/main arm64 python3-appdirs all 1.4.4-4 [12.5 kB] Get: 165 http://deb.debian.org/debian trixie/main arm64 python3-six all 1.16.0-6 [16.3 kB] Get: 166 http://deb.debian.org/debian trixie/main arm64 python3-asttokens all 2.4.1-1 [20.6 kB] Get: 167 http://deb.debian.org/debian trixie/main arm64 python3-astunparse all 1.6.3-2 [13.8 kB] Get: 168 http://deb.debian.org/debian trixie/main arm64 python3-attr all 23.2.0-2 [65.5 kB] Get: 169 http://deb.debian.org/debian trixie/main arm64 python3-tz all 2024.1-2 [30.9 kB] Get: 170 http://deb.debian.org/debian trixie/main arm64 python3-babel all 2.14.0-1 [111 kB] Get: 171 http://deb.debian.org/debian trixie/main arm64 python3-webencodings all 0.5.1-5 [11.1 kB] Get: 172 http://deb.debian.org/debian trixie/main arm64 python3-html5lib all 1.1-6 [90.5 kB] Get: 173 http://deb.debian.org/debian trixie/main arm64 python3-bleach all 6.1.0-2 [50.7 kB] Get: 174 http://deb.debian.org/debian trixie/main arm64 python3-brotli arm64 1.1.0-2+b3 [316 kB] Get: 175 http://deb.debian.org/debian trixie/main arm64 python3-soupsieve all 2.5-1 [38.1 kB] Get: 176 http://deb.debian.org/debian trixie/main arm64 python3-bs4 all 4.12.3-1 [133 kB] Get: 177 http://deb.debian.org/debian trixie/main arm64 python3-typing-extensions all 4.10.0-1 [66.2 kB] Get: 178 http://deb.debian.org/debian trixie/main arm64 python3-bytecode all 0.15.1-3 [41.5 kB] Get: 179 http://deb.debian.org/debian trixie/main arm64 python3-certifi all 2023.11.17-1 [155 kB] Get: 180 http://deb.debian.org/debian trixie/main arm64 python3-cffi-backend arm64 1.16.0-2+b2 [109 kB] Get: 181 http://deb.debian.org/debian trixie/main arm64 python3-chardet all 5.2.0+dfsg-1 [107 kB] Get: 182 http://deb.debian.org/debian trixie/main arm64 python3-charset-normalizer all 3.3.2-1 [51.6 kB] Get: 183 http://deb.debian.org/debian trixie/main arm64 python3-traitlets all 5.5.0-2 [90.7 kB] Get: 184 http://deb.debian.org/debian trixie/main arm64 python3-comm all 0.2.1-1 [8104 B] Get: 185 http://deb.debian.org/debian trixie/main arm64 python3-numpy arm64 1:1.24.2-2 [4122 kB] Get: 186 http://deb.debian.org/debian trixie/main arm64 python3-contourpy arm64 1.0.7-3 [247 kB] Get: 187 http://deb.debian.org/debian trixie/main arm64 python3-coverage arm64 7.2.7+dfsg1-1+b1 [170 kB] Get: 188 http://deb.debian.org/debian trixie/main arm64 python3-cycler all 0.12.1-1 [9496 B] Get: 189 http://deb.debian.org/debian trixie/main arm64 python3-dateutil all 2.9.0-2 [79.4 kB] Get: 190 http://deb.debian.org/debian trixie/main arm64 python3-pydevd arm64 2.10.0+ds-10 [565 kB] Get: 191 http://deb.debian.org/debian trixie/main arm64 python3-debugpy all 1.8.0+ds-4 [66.7 kB] Get: 192 http://deb.debian.org/debian trixie/main arm64 python3-decorator all 5.1.1-5 [15.1 kB] Get: 193 http://deb.debian.org/debian trixie/main arm64 python3-defusedxml all 0.7.1-2 [43.3 kB] Get: 194 http://deb.debian.org/debian trixie/main arm64 python3-roman all 3.3-3 [9880 B] Get: 195 http://deb.debian.org/debian trixie/main arm64 python3-docutils all 0.20.1+dfsg-3 [389 kB] Get: 196 http://deb.debian.org/debian trixie/main arm64 python3-entrypoints all 0.4-2 [7184 B] Get: 197 http://deb.debian.org/debian trixie/main arm64 python3-executing all 2.0.1-0.1 [22.7 kB] Get: 198 http://deb.debian.org/debian trixie/main arm64 python3-fastjsonschema all 2.19.1-1 [21.3 kB] Get: 199 http://deb.debian.org/debian trixie/main arm64 python3-scipy arm64 1.11.4-6 [17.5 MB] Get: 200 http://deb.debian.org/debian trixie/main arm64 python3-ufolib2 all 0.16.0+dfsg1-1 [32.9 kB] Get: 201 http://deb.debian.org/debian trixie/main arm64 python3-mpmath all 1.3.0-1 [419 kB] Get: 202 http://deb.debian.org/debian trixie/main arm64 python3-sympy all 1.12-7 [3869 kB] Get: 203 http://deb.debian.org/debian trixie/main arm64 python3-fs all 2.4.16-4 [95.4 kB] Get: 204 http://deb.debian.org/debian trixie/main arm64 python3-lxml arm64 5.1.0-1 [1810 kB] Get: 205 http://deb.debian.org/debian trixie/main arm64 python3-lz4 arm64 4.0.2+dfsg-1+b3 [26.6 kB] Get: 206 http://deb.debian.org/debian trixie/main arm64 unicode-data all 15.1.0-1 [8547 kB] Get: 207 http://deb.debian.org/debian trixie/main arm64 python3-fonttools arm64 4.46.0-1 [1510 kB] Get: 208 http://deb.debian.org/debian trixie/main arm64 python3-packaging all 24.0-1 [45.5 kB] Get: 209 http://deb.debian.org/debian trixie/main arm64 python3-pathspec all 0.12.1-1 [28.1 kB] Get: 210 http://deb.debian.org/debian trixie/main arm64 python3-pluggy all 1.5.0-1 [26.9 kB] Get: 211 http://deb.debian.org/debian trixie/main arm64 python3-trove-classifiers all 2024.1.31-1 [9968 B] Get: 212 http://deb.debian.org/debian trixie/main arm64 python3-hatchling all 1.24.2-1 [53.2 kB] Get: 213 http://deb.debian.org/debian trixie/main arm64 python3-setuptools-scm all 8.0.4-2 [39.5 kB] Get: 214 http://deb.debian.org/debian trixie/main arm64 python3-hatch-vcs all 0.4.0-1 [8336 B] Get: 215 http://deb.debian.org/debian trixie/main arm64 python3-idna all 3.6-2 [37.0 kB] Get: 216 http://deb.debian.org/debian trixie/main arm64 python3-imagesize all 1.4.1-1 [6688 B] Get: 217 http://deb.debian.org/debian trixie/main arm64 python3-parso all 0.8.3-1 [67.4 kB] Get: 218 http://deb.debian.org/debian trixie/main arm64 python3-typeshed all 0.0~git20231111.6764465-3 [1258 kB] Get: 219 http://deb.debian.org/debian trixie/main arm64 python3-jedi all 0.19.1+ds1-1 [691 kB] Get: 220 http://deb.debian.org/debian trixie/main arm64 python3-matplotlib-inline all 0.1.6-2 [8652 B] Get: 221 http://deb.debian.org/debian trixie/main arm64 python3-ptyprocess all 0.7.0-5 [14.7 kB] Get: 222 http://deb.debian.org/debian trixie/main arm64 python3-pexpect all 4.9-2 [55.5 kB] Get: 223 http://deb.debian.org/debian trixie/main arm64 python3-wcwidth all 0.2.13+dfsg1-1 [24.9 kB] Get: 224 http://deb.debian.org/debian trixie/main arm64 python3-prompt-toolkit all 3.0.43-1 [276 kB] Get: 225 http://deb.debian.org/debian trixie/main arm64 python3-pygments all 2.17.2+dfsg-1 [818 kB] Get: 226 http://deb.debian.org/debian trixie/main arm64 python3-pure-eval all 0.2.2-2 [11.0 kB] Get: 227 http://deb.debian.org/debian trixie/main arm64 python3-stack-data all 0.6.3-1 [21.6 kB] Get: 228 http://deb.debian.org/debian trixie/main arm64 python3-ipython all 8.20.0-1 [556 kB] Get: 229 http://deb.debian.org/debian trixie/main arm64 python3-platformdirs all 4.2.1-1 [16.0 kB] Get: 230 http://deb.debian.org/debian trixie/main arm64 python3-jupyter-core all 5.3.2-1 [31.5 kB] Get: 231 http://deb.debian.org/debian trixie/main arm64 python3-nest-asyncio all 1.5.4-1 [6248 B] Get: 232 http://deb.debian.org/debian trixie/main arm64 python3-tornado arm64 6.4.0-1 [347 kB] Get: 233 http://deb.debian.org/debian trixie/main arm64 python3-py all 1.11.0-2 [88.7 kB] Get: 234 http://deb.debian.org/debian trixie/main arm64 python3-zmq arm64 24.0.1-5+b1 [329 kB] Get: 235 http://deb.debian.org/debian trixie/main arm64 python3-jupyter-client all 7.4.9-2 [103 kB] Get: 236 http://deb.debian.org/debian trixie/main arm64 python3-psutil arm64 5.9.8-2 [225 kB] Get: 237 http://deb.debian.org/debian trixie/main arm64 python3-ipykernel all 6.29.3-1 [102 kB] Get: 238 http://deb.debian.org/debian trixie/main arm64 python3-markupsafe arm64 2.1.5-1 [14.6 kB] Get: 239 http://deb.debian.org/debian trixie/main arm64 python3-jinja2 all 3.1.3-1 [119 kB] Get: 240 http://deb.debian.org/debian trixie/main arm64 python3-joblib all 1.3.2-2 [218 kB] Get: 241 http://deb.debian.org/debian trixie/main arm64 python3-rpds-py arm64 0.12.0-3 [241 kB] Get: 242 http://deb.debian.org/debian trixie/main arm64 python3-referencing all 0.31.0-1 [22.2 kB] Get: 243 http://deb.debian.org/debian trixie/main arm64 python3-jsonschema-specifications all 2023.12.1-1 [8976 B] Get: 244 http://deb.debian.org/debian trixie/main arm64 python3-jsonschema all 4.19.2-2 [71.2 kB] Get: 245 http://deb.debian.org/debian trixie/main arm64 python3-jupyterlab-pygments all 0.2.2-3 [6096 B] Get: 246 http://deb.debian.org/debian trixie/main arm64 python3-kiwisolver arm64 1.4.5-1 [75.0 kB] Get: 247 http://deb.debian.org/debian trixie/main arm64 python3-lxml-html-clean all 0.1.1-1 [13.0 kB] Get: 248 http://deb.debian.org/debian trixie/main arm64 python3-pil arm64 10.3.0-2 [552 kB] Get: 249 http://deb.debian.org/debian trixie/main arm64 python3-tk arm64 3.12.3-1 [110 kB] Get: 250 http://deb.debian.org/debian trixie/main arm64 python3-pil.imagetk arm64 10.3.0-2 [80.0 kB] Get: 251 http://deb.debian.org/debian trixie/main arm64 python3-pyparsing all 3.1.2-1 [146 kB] Get: 252 http://deb.debian.org/debian trixie/main arm64 python3-matplotlib arm64 3.6.3-1+b2 [7970 kB] Get: 253 http://deb.debian.org/debian trixie/main arm64 sphinx-rtd-theme-common all 2.0.0+dfsg-1 [1021 kB] Get: 254 http://deb.debian.org/debian trixie/main arm64 sphinx-common all 7.2.6-6 [702 kB] Get: 255 http://deb.debian.org/debian trixie/main arm64 python3-urllib3 all 1.26.18-2 [116 kB] Get: 256 http://deb.debian.org/debian trixie/main arm64 python3-requests all 2.31.0+dfsg-1 [68.6 kB] Get: 257 http://deb.debian.org/debian trixie/main arm64 python3-snowballstemmer all 2.2.0-4 [58.0 kB] Get: 258 http://deb.debian.org/debian trixie/main arm64 python3-sphinx all 7.2.6-6 [552 kB] Get: 259 http://deb.debian.org/debian trixie/main arm64 python3-sphinxcontrib.jquery all 4.1-5 [7348 B] Get: 260 http://deb.debian.org/debian trixie/main arm64 python3-sphinx-rtd-theme all 2.0.0+dfsg-1 [28.3 kB] Get: 261 http://deb.debian.org/debian trixie/main arm64 python3-msmb-theme all 1.2.0-4 [33.8 kB] Get: 262 http://deb.debian.org/debian trixie/main arm64 python3-nbformat all 5.9.1-1 [45.1 kB] Get: 263 http://deb.debian.org/debian trixie/main arm64 python3-nbclient all 0.8.0-1 [64.0 kB] Get: 264 http://deb.debian.org/debian trixie/main arm64 python3-pandocfilters all 1.5.1-1 [23.7 kB] Get: 265 http://deb.debian.org/debian trixie/main arm64 python3-tinycss2 all 1.2.1-2 [21.9 kB] Get: 266 http://deb.debian.org/debian trixie/main arm64 python3-nbconvert all 6.5.3-5 [163 kB] Get: 267 http://deb.debian.org/debian trixie/main arm64 python3-networkx all 2.8.8-2 [1425 kB] Get: 268 http://deb.debian.org/debian trixie/main arm64 python3-numexpr arm64 2.9.0-1 [91.8 kB] Get: 269 http://deb.debian.org/debian trixie/main arm64 python3-tabulate all 0.8.10-1 [38.8 kB] Get: 270 http://deb.debian.org/debian trixie/main arm64 python3-numpydoc all 1.6.0-2 [49.6 kB] Get: 271 http://deb.debian.org/debian trixie/main arm64 python3-pandas-lib arm64 2.1.4+dfsg-5 [6620 kB] Get: 272 http://deb.debian.org/debian trixie/main arm64 python3-pandas all 2.1.4+dfsg-5 [3015 kB] Get: 273 http://deb.debian.org/debian trixie/main arm64 python3-threadpoolctl all 3.1.0-1 [21.2 kB] Get: 274 http://deb.debian.org/debian trixie/main arm64 python3-sklearn-lib arm64 1.4.1.post1+dfsg-1 [5691 kB] Get: 275 http://deb.debian.org/debian trixie/main arm64 python3-sklearn all 1.4.1.post1+dfsg-1 [2246 kB] Get: 276 http://deb.debian.org/debian trixie/main arm64 python3-tables-lib arm64 3.7.0-10+b1 [583 kB] Get: 277 http://deb.debian.org/debian trixie/main arm64 python3-tables all 3.7.0-10 [338 kB] Fetched 178 MB in 1s (201 MB/s) debconf: delaying package configuration, since apt-utils is not installed dpkg: libdb5.3:arm64: dependency problems, but removing anyway as you requested: libperl5.38:arm64 depends on libdb5.3. libpam-modules:arm64 depends on libdb5.3. (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 ... 19915 files and directories currently installed.) Removing libdb5.3:arm64 (5.3.28+dfsg2-4+b1) ... Selecting previously unselected package libdb5.3t64:arm64. (Reading database ... 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Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:arm64 (8.2-4) ... Selecting previously unselected package libpython3.11-stdlib:arm64. Preparing to unpack .../6-libpython3.11-stdlib_3.11.9-1_arm64.deb ... Unpacking libpython3.11-stdlib:arm64 (3.11.9-1) ... Selecting previously unselected package python3.11. Preparing to unpack .../7-python3.11_3.11.9-1_arm64.deb ... Unpacking python3.11 (3.11.9-1) ... 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Setting up libpipeline1:arm64 (1.5.7-2) ... Setting up libgraphite2-3:arm64 (1.3.14-2) ... Setting up liblcms2-2:arm64 (2.14-2+b1) ... Setting up libnorm1t64:arm64 (1.5.9+dfsg-3.1) ... Setting up libsharpyuv0:arm64 (1.3.2-0.4+b1) ... Setting up libxau6:arm64 (1:1.0.9-1+b1) ... Setting up fonts-lato (2.015-1) ... Setting up fonts-mathjax (2.7.9+dfsg-1) ... Setting up libsodium23:arm64 (1.0.18-1+b1) ... Setting up libicu72:arm64 (72.1-4+b1) ... Setting up liblerc4:arm64 (4.0.0+ds-4+b1) ... Setting up bsdextrautils (2.40-8) ... Setting up libjs-mathjax (2.7.9+dfsg-1) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up fonts-lyx (2.4.0~RC4-1) ... Setting up libdebhelper-perl (13.15.3) ... Setting up libbrotli1:arm64 (1.1.0-2+b3) ... Setting up libmagic1t64:arm64 (1:5.45-3) ... Setting up libpython3.12-minimal:arm64 (3.12.3-1) ... Setting up x11-common (1:7.7+23) ... invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libpsl5t64:arm64 (0.21.2-1.1) ... Setting up libnghttp2-14:arm64 (1.59.0-1) ... Setting up libdeflate0:arm64 (1.20-1) ... Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... Setting up libqhull-r8.0:arm64 (2020.2-6+b1) ... Setting up liblzo2-2:arm64 (2.10-2+b1) ... Setting up libblis4-serial:arm64 (0.9.0-1+b2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blis-serial/libblis.so.4 to provide /usr/lib/aarch64-linux-gnu/libblis.so.4 (libblis.so.4-aarch64-linux-gnu) in auto mode update-alternatives: using /usr/lib/aarch64-linux-gnu/blis-serial/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode Setting up file (1:5.45-3) ... Setting up libjbig0:arm64 (2.1-6.1+b1) ... Setting up libaec0:arm64 (1.1.3-1) ... Setting up libsource-highlight-common (3.1.9-4.3) ... Setting up libelf1t64:arm64 (0.191-1+b1) ... Setting up python-babel-localedata (2.14.0-1) ... Setting up libsnappy1v5:arm64 (1.1.10-1+b1) ... Setting up libdw1t64:arm64 (0.191-1+b1) ... Setting up libsasl2-modules-db:arm64 (2.1.28+dfsg1-4+b1) ... Setting up tzdata (2024a-3) ... Current default time zone: 'Etc/UTC' Local time is now: Thu May 2 14:00:32 UTC 2024. Universal Time is now: Thu May 2 14:00:32 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up unicode-data (15.1.0-1) ... Setting up libpgm-5.3-0t64:arm64 (5.3.128~dfsg-2.1) ... Setting up autotools-dev (20220109.1) ... Setting up libglib2.0-0t64:arm64 (2.78.4-7) ... No schema files found: doing nothing. Setting up libexpat1-dev:arm64 (2.6.2-1) ... Setting up libjpeg62-turbo:arm64 (1:2.1.5-3) ... Setting up libx11-data (2:1.8.7-1) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b4) ... Setting up libfribidi0:arm64 (1.0.13-3+b1) ... Setting up libimagequant0:arm64 (2.18.0-1+b1) ... Setting up libproc2-0:arm64 (2:4.0.4-4) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:arm64 (1.6.43-5) ... Setting up libtcl8.6:arm64 (8.6.14+dfsg-1) ... Setting up autopoint (0.21-14) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libbabeltrace1:arm64 (1.5.11-3+b6) ... Setting up libsasl2-2:arm64 (2.1.28+dfsg1-4+b1) ... Setting up libgfortran5:arm64 (14-20240330-1) ... Setting up autoconf (2.71-3) ... Setting up libwebp7:arm64 (1.3.2-0.4+b1) ... Setting up zlib1g-dev:arm64 (1:1.3.dfsg-3.1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.22) ... Setting up libtiff6:arm64 (4.5.1+git230720-4) ... Setting up libuchardet0:arm64 (0.0.8-1+b1) ... Setting up procps (2:4.0.4-4) ... Setting up python-tinycss2-common (1.2.1-2) ... Setting up libjson-perl (4.10000-1) ... Setting up libblosc1:arm64 (1.21.5+ds-1+b1) ... Setting up libopenjp2-7:arm64 (2.5.0-2+b3) ... Setting up libsub-override-perl (0.10-1) ... Setting up netbase (6.4) ... Setting up sgml-base (1.31) ... Setting up libssh2-1t64:arm64 (1.11.0-4.1+b2) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up python-matplotlib-data (3.6.3-1) ... Setting up openssl (3.2.1-3) ... Setting up libwebpmux3:arm64 (1.3.2-0.4+b1) ... Setting up libbsd0:arm64 (0.12.2-1) ... Setting up readline-common (8.2-4) ... Setting up libxml2:arm64 (2.9.14+dfsg-1.3+b3) ... Setting up python-tables-data (3.7.0-10) ... Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... Setting up sphinx-rtd-theme-common (2.0.0+dfsg-1) ... Setting up libsz2:arm64 (1.1.3-1) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up python3.12-minimal (3.12.3-1) ... Setting up libxdmcp6:arm64 (1:1.1.2-3+b1) ... Setting up liblapack3:arm64 (3.12.0-3) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up libxcb1:arm64 (1.15-1) ... Setting up gettext (0.21-14+b1) ... Setting up libzmq5:arm64 (4.3.5-1+b2) ... Setting up libtool (2.4.7-7) ... Setting up fontconfig-config (2.15.0-1.1) ... Setting up libwebpdemux2:arm64 (1.3.2-0.4+b1) ... Setting up libsource-highlight4t64:arm64 (3.1.9-4.3) ... Setting up libldap-2.5-0:arm64 (2.5.13+dfsg-5+b3) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libfreetype6:arm64 (2.13.2+dfsg-1+b4) ... Setting up ucf (3.0043+nmu1) ... Setting up libjs-sphinxdoc (7.2.6-6) ... Setting up libreadline8t64:arm64 (8.2-4) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up groff-base (1.23.0-3+b1) ... Setting up xml-core (0.19) ... Setting up libxslt1.1:arm64 (1.1.35-1+b1) ... Setting up libx11-6:arm64 (2:1.8.7-1+b1) ... Setting up libharfbuzz0b:arm64 (8.3.0-2+b1) ... Setting up libfontconfig1:arm64 (2.15.0-1.1) ... Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1+b1) ... Setting up libpython3.12-stdlib:arm64 (3.12.3-1) ... Setting up libxrender1:arm64 (1:0.9.10-1.1+b1) ... Setting up libdebuginfod-common (0.191-1) ... Setting up libcurl4t64:arm64 (8.7.1-3) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:arm64 (3.11.9-1) ... Setting up python3.12 (3.12.3-1) ... Setting up libpython3.11t64:arm64 (3.11.9-1) ... Setting up libcurl3t64-gnutls:arm64 (8.7.1-3) ... Setting up libxext6:arm64 (2:1.3.4-1+b1) ... Setting up man-db (2.12.0-3) ... Not building database; man-db/auto-update is not 'true'. Setting up libpython3.12t64:arm64 (3.12.3-1) ... Setting up libpython3.11-dev:arm64 (3.11.9-1) ... Setting up libraqm0:arm64 (0.10.1-1+b1) ... Setting up sphinx-common (7.2.6-6) ... Setting up libhdf5-103-1:arm64 (1.10.10+repack-3+b1) ... Setting up libxss1:arm64 (1:1.2.3-1+b1) ... Setting up libpython3-stdlib:arm64 (3.11.8-1) ... Setting up python3.11 (3.11.9-1) ... Setting up libdebuginfod1t64:arm64 (0.191-1+b1) ... Setting up libxft2:arm64 (2.3.6-1+b1) ... Setting up libpython3-dev:arm64 (3.11.8-1) ... Setting up python3.11-dev (3.11.9-1) ... Setting up libtk8.6:arm64 (8.6.14-1) ... Setting up debhelper (13.15.3) ... Setting up python3 (3.11.8-1) ... Setting up libpython3.12-dev:arm64 (3.12.3-1) ... Setting up python3-pandocfilters (1.5.1-1) ... Setting up python3-markupsafe (2.1.5-1) ... Setting up python3-webencodings (0.5.1-5) ... Setting up python3-platformdirs (4.2.1-1) ... Setting up python3-psutil (5.9.8-2) ... Setting up python3-tz (2024.1-2) ... 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Setting up python3-urllib3 (1.26.18-2) ... Setting up python3-pluggy (1.5.0-1) ... Setting up python3-rpds-py (0.12.0-3) ... Setting up python3-fastjsonschema (2.19.1-1) ... Setting up python3-trove-classifiers (2024.1.31-1) ... Setting up python3-lxml:arm64 (5.1.0-1) ... Setting up python3-traitlets (5.5.0-2) ... Setting up python3-dateutil (2.9.0-2) ... Setting up python3-mpmath (1.3.0-1) ... Setting up python3-pathspec (0.12.1-1) ... Setting up python3-lib2to3 (3.12.3-1) ... Setting up python3-appdirs (1.4.4-4) ... Setting up python3-soupsieve (2.5-1) ... Setting up python3-cffi-backend:arm64 (1.16.0-2+b2) ... Setting up python3-imagesize (1.4.1-1) ... Setting up python3-ptyprocess (0.7.0-5) ... Setting up python3-pkg-resources (68.1.2-2) ... Setting up python3-entrypoints (0.4-2) ... Setting up python3-prompt-toolkit (3.0.43-1) ... Setting up python3-distutils (3.12.3-1) ... python3.12: can't get files for byte-compilation Setting up python3-sympy (1.12-7) ... Setting up python3-attr (23.2.0-2) ... Setting up python3-tornado (6.4.0-1) ... Setting up python3-pure-eval (0.2.2-2) ... Setting up tk8.6-blt2.5 (2.5.3+dfsg-7) ... Setting up python3-astunparse (1.6.3-2) ... Setting up python3-zombie-imp (0.0.2-2) ... Setting up python3-tinycss2 (1.2.1-2) ... Setting up python3-setuptools (68.1.2-2) ... Setting up python3-py (1.11.0-2) ... Setting up python3-joblib (1.3.2-2) ... Setting up python3-parso (0.8.3-1) ... Setting up python3-babel (2.14.0-1) ... update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up python3-lz4 (4.0.2+dfsg-1+b3) ... Setting up python3-defusedxml (0.7.1-2) ... Setting up python3-asttokens (2.4.1-1) ... Setting up python3-charset-normalizer (3.3.2-1) ... Setting up python3-alabaster (0.7.12-1) ... Setting up blt (2.5.3+dfsg-7) ... Setting up python3-threadpoolctl (3.1.0-1) ... Setting up python3-tabulate (0.8.10-1) ... Setting up python3-all (3.11.8-1) ... Setting up python3-coverage (7.2.7+dfsg1-1+b1) ... Setting up python3-tk:arm64 (3.12.3-1) ... Setting up python3-networkx (2.8.8-2) ... /usr/lib/python3/dist-packages/networkx/readwrite/tests/test_gml.py:556: SyntaxWarning: invalid octal escape sequence '\420' "graph [edge [ source u'u\4200' target u'u\4200' ] " /usr/lib/python3/dist-packages/networkx/readwrite/tests/test_gml.py:557: SyntaxWarning: invalid octal escape sequence '\420' + "node [ id u'u\4200' label b ] ]" Setting up python3-setuptools-scm (8.0.4-2) ... Setting up python3-bs4 (4.12.3-1) ... Setting up python3-bleach (6.1.0-2) ... Setting up python3-matplotlib-inline (0.1.6-2) ... Setting up python3-comm (0.2.1-1) ... Setting up python3-fs (2.4.16-4) ... Setting up python3-pygments (2.17.2+dfsg-1) ... Setting up python3-chardet (5.2.0+dfsg-1) ... Setting up python3-pil.imagetk:arm64 (10.3.0-2) ... Setting up python3-executing (2.0.1-0.1) ... Setting up python3-pexpect (4.9-2) ... Setting up python3-zmq (24.0.1-5+b1) ... Setting up python3-dev (3.11.8-1) ... Setting up python3-requests (2.31.0+dfsg-1) ... Setting up python3-numpy (1:1.24.2-2) ... Setting up python3-lxml-html-clean (0.1.1-1) ... Setting up cython3-legacy (0.29.37-2) ... Setting up python3-contourpy (1.0.7-3) ... Setting up python3-hatchling (1.24.2-1) ... Setting up python3-pydevd (2.10.0+ds-10) ... Setting up python3-stack-data (0.6.3-1) ... Setting up python3-jupyter-core (5.3.2-1) ... Setting up python3-hatch-vcs (0.4.0-1) ... Setting up python3-referencing (0.31.0-1) ... Setting up dh-python (6.20240422) ... Setting up python3-all-dev (3.11.8-1) ... Setting up python3-scipy (1.11.4-6) ... Setting up python3-jedi (0.19.1+ds1-1) ... Setting up python3-tables-lib (3.7.0-10+b1) ... Setting up python3-pandas-lib:arm64 (2.1.4+dfsg-5) ... Setting up python3-sklearn-lib:arm64 (1.4.1.post1+dfsg-1) ... Setting up python3-debugpy (1.8.0+ds-4) ... Setting up python3-jupyterlab-pygments (0.2.2-3) ... Setting up python3-pandas (2.1.4+dfsg-5) ... Setting up python3-ipython (8.20.0-1) ... Setting up python3-sklearn (1.4.1.post1+dfsg-1) ... Setting up python3-numexpr (2.9.0-1) ... Setting up python3-jupyter-client (7.4.9-2) ... Setting up python3-jsonschema-specifications (2023.12.1-1) ... Setting up python3-tables (3.7.0-10) ... Setting up python3-jsonschema (4.19.2-2) ... Setting up python3-ipykernel (6.29.3-1) ... Setting up python3-nbformat (5.9.1-1) ... Setting up python3-nbclient (0.8.0-1) ... Setting up python3-nbconvert (6.5.3-5) ... Setting up python3-fonttools (4.46.0-1) ... Setting up python3-ufolib2 (0.16.0+dfsg1-1) ... Setting up python3-matplotlib (3.6.3-1+b2) ... Processing triggers for libc-bin (2.37-18) ... Processing triggers for sgml-base (1.31) ... Setting up docutils-common (0.20.1+dfsg-3) ... Processing triggers for sgml-base (1.31) ... Setting up python3-docutils (0.20.1+dfsg-3) ... Setting up python3-sphinx (7.2.6-6) ... Setting up python3-sphinxcontrib.jquery (4.1-5) ... Setting up python3-numpydoc (1.6.0-2) ... Setting up python3-sphinx-rtd-theme (2.0.0+dfsg-1) ... Setting up python3-msmb-theme (1.2.0-4) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/4115798/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/4115798/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/mdtraj-1.9.9/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../mdtraj_1.9.9-1_source.changes dpkg-buildpackage: info: source package mdtraj dpkg-buildpackage: info: source version 1.9.9-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 dpkg-source: info: using options from mdtraj-1.9.9/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/ debian/rules clean dh clean --with sphinxdoc --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/mdtraj-1.9.9' dh_auto_clean || /bin/true pybuild --clean -i python{version} -p "3.12 3.11" I: pybuild base:311: python3.12 setup.py clean Using built-in specs. COLLECT_GCC=/usr/bin/aarch64-linux-gnu-gcc COLLECT_LTO_WRAPPER=/usr/libexec/gcc/aarch64-linux-gnu/13/lto-wrapper OFFLOAD_TARGET_NAMES=nvptx-none OFFLOAD_TARGET_DEFAULT=1 Target: aarch64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 13.2.0-23' --with-bugurl=file:///usr/share/doc/gcc-13/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-13 --program-prefix=aarch64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libquadmath --disable-libquadmath-support --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --enable-fix-cortex-a53-843419 --disable-werror --enable-offload-targets=nvptx-none=/build/reproducible-path/gcc-13-13.2.0/debian/tmp-nvptx/usr --enable-offload-defaulted --without-cuda-driver --enable-checking=release --build=aarch64-linux-gnu --host=aarch64-linux-gnu --target=aarch64-linux-gnu Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 13.2.0 (Debian 13.2.0-23) /build/reproducible-path/mdtraj-1.9.9/basesetup.py:451: 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 SSE2 support... Did not detect SSE2 support Attempting to autodetect SSE3 support... Did not detect SSE3 support Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support Attempting to autodetect NEON support... Compiler supports NEON [ 1/12] Cythonizing mdtraj/formats/binpos/binpos.pyx [ 2/12] Cythonizing mdtraj/formats/dcd/dcd.pyx [ 3/12] Cythonizing mdtraj/formats/dtr/dtr.pyx [ 4/12] Cythonizing mdtraj/formats/tng/tng.pyx [ 5/12] Cythonizing mdtraj/formats/xtc/trr.pyx [ 6/12] Cythonizing mdtraj/formats/xtc/xtc.pyx [ 7/12] Cythonizing mdtraj/geometry/drid.pyx [ 8/12] Cythonizing mdtraj/geometry/neighborlist.pyx [ 9/12] Cythonizing mdtraj/geometry/neighbors.pyx [10/12] Cythonizing mdtraj/geometry/src/_geometry.pyx [11/12] Cythonizing mdtraj/rmsd/_lprmsd.pyx [12/12] Cythonizing mdtraj/rmsd/_rmsd.pyx running clean removing '/build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build' (and everything under it) 'build/bdist.linux-aarch64' does not exist -- can't clean it 'build/scripts-3.12' does not exist -- can't clean it I: pybuild base:311: python3.11 setup.py clean Using built-in specs. COLLECT_GCC=/usr/bin/aarch64-linux-gnu-gcc COLLECT_LTO_WRAPPER=/usr/libexec/gcc/aarch64-linux-gnu/13/lto-wrapper OFFLOAD_TARGET_NAMES=nvptx-none OFFLOAD_TARGET_DEFAULT=1 Target: aarch64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 13.2.0-23' --with-bugurl=file:///usr/share/doc/gcc-13/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-13 --program-prefix=aarch64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libquadmath --disable-libquadmath-support --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --enable-fix-cortex-a53-843419 --disable-werror --enable-offload-targets=nvptx-none=/build/reproducible-path/gcc-13-13.2.0/debian/tmp-nvptx/usr --enable-offload-defaulted --without-cuda-driver --enable-checking=release --build=aarch64-linux-gnu --host=aarch64-linux-gnu --target=aarch64-linux-gnu Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 13.2.0 (Debian 13.2.0-23) /build/reproducible-path/mdtraj-1.9.9/basesetup.py:451: 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 SSE2 support... Did not detect SSE2 support Attempting to autodetect SSE3 support... Did not detect SSE3 support Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support Attempting to autodetect NEON support... Compiler supports NEON [ 1/12] Cythonizing mdtraj/formats/dcd/dcd.pyx [ 2/12] Cythonizing mdtraj/geometry/drid.pyx [ 3/12] Cythonizing mdtraj/geometry/neighborlist.pyx [ 4/12] Cythonizing mdtraj/geometry/neighbors.pyx [ 5/12] Cythonizing mdtraj/geometry/src/_geometry.pyx [ 6/12] Cythonizing mdtraj/rmsd/_lprmsd.pyx [ 7/12] Cythonizing mdtraj/formats/binpos/binpos.pyx [ 8/12] Cythonizing mdtraj/formats/dtr/dtr.pyx [ 9/12] Cythonizing mdtraj/formats/tng/tng.pyx [10/12] Cythonizing mdtraj/formats/xtc/trr.pyx [11/12] Cythonizing mdtraj/formats/xtc/xtc.pyx [12/12] Cythonizing mdtraj/rmsd/_rmsd.pyx running clean removing '/build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build' (and everything under it) 'build/bdist.linux-aarch64' does not exist -- can't clean it 'build/scripts-3.11' does not exist -- can't clean it rm -rf .pybuild/ find . -name \*.pyc -exec rm {} \; 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__ .pybuild find . -name "lib*.a" -delete make[1]: Leaving directory '/build/reproducible-path/mdtraj-1.9.9' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/python3-mdtraj.substvars debian/python-mdtraj-doc.substvars debian/files rm -fr -- debian/python3-mdtraj/ debian/tmp/ debian/python-mdtraj-doc/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a \( -name autom4te.cache -o -name __pycache__ \) -prune -exec rm -rf {} + \) \) debian/rules binary dh binary --with sphinxdoc --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild pybuild --configure -i python{version} -p "3.12 3.11" I: pybuild base:311: python3.12 setup.py config Using built-in specs. COLLECT_GCC=/usr/bin/aarch64-linux-gnu-gcc COLLECT_LTO_WRAPPER=/usr/libexec/gcc/aarch64-linux-gnu/13/lto-wrapper OFFLOAD_TARGET_NAMES=nvptx-none OFFLOAD_TARGET_DEFAULT=1 Target: aarch64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 13.2.0-23' --with-bugurl=file:///usr/share/doc/gcc-13/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-13 --program-prefix=aarch64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libquadmath --disable-libquadmath-support --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --enable-fix-cortex-a53-843419 --disable-werror --enable-offload-targets=nvptx-none=/build/reproducible-path/gcc-13-13.2.0/debian/tmp-nvptx/usr --enable-offload-defaulted --without-cuda-driver --enable-checking=release --build=aarch64-linux-gnu --host=aarch64-linux-gnu --target=aarch64-linux-gnu Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 13.2.0 (Debian 13.2.0-23) /build/reproducible-path/mdtraj-1.9.9/basesetup.py:451: 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 SSE2 support... Did not detect SSE2 support Attempting to autodetect SSE3 support... Did not detect SSE3 support Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support Attempting to autodetect NEON support... Compiler supports NEON [ 1/12] 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:311: python3.11 setup.py config Using built-in specs. COLLECT_GCC=/usr/bin/aarch64-linux-gnu-gcc COLLECT_LTO_WRAPPER=/usr/libexec/gcc/aarch64-linux-gnu/13/lto-wrapper OFFLOAD_TARGET_NAMES=nvptx-none OFFLOAD_TARGET_DEFAULT=1 Target: aarch64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 13.2.0-23' --with-bugurl=file:///usr/share/doc/gcc-13/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-13 --program-prefix=aarch64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libquadmath --disable-libquadmath-support --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --enable-fix-cortex-a53-843419 --disable-werror --enable-offload-targets=nvptx-none=/build/reproducible-path/gcc-13-13.2.0/debian/tmp-nvptx/usr --enable-offload-defaulted --without-cuda-driver --enable-checking=release --build=aarch64-linux-gnu --host=aarch64-linux-gnu --target=aarch64-linux-gnu Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 13.2.0 (Debian 13.2.0-23) /build/reproducible-path/mdtraj-1.9.9/basesetup.py:451: 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 SSE2 support... Did not detect SSE2 support Attempting to autodetect SSE3 support... Did not detect SSE3 support Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support Attempting to autodetect NEON support... Compiler supports NEON [ 1/12] Cythonizing mdtraj/formats/dcd/dcd.pyx [ 2/12] Cythonizing mdtraj/geometry/drid.pyx [ 3/12] Cythonizing mdtraj/geometry/neighborlist.pyx [ 4/12] Cythonizing mdtraj/geometry/neighbors.pyx [ 5/12] Cythonizing mdtraj/geometry/src/_geometry.pyx [ 6/12] Cythonizing mdtraj/rmsd/_lprmsd.pyx [ 7/12] Cythonizing mdtraj/formats/binpos/binpos.pyx [ 8/12] Cythonizing mdtraj/formats/dtr/dtr.pyx [ 9/12] Cythonizing mdtraj/formats/tng/tng.pyx [10/12] Cythonizing mdtraj/formats/xtc/trr.pyx [11/12] Cythonizing mdtraj/formats/xtc/xtc.pyx [12/12] Cythonizing mdtraj/rmsd/_rmsd.pyx running config debian/rules override_dh_auto_build-indep make[1]: Entering directory '/build/reproducible-path/mdtraj-1.9.9' dh_auto_build pybuild --build -i python{version} -p "3.12 3.11" I: pybuild base:311: /usr/bin/python3.12 setup.py build Using built-in specs. COLLECT_GCC=/usr/bin/aarch64-linux-gnu-gcc COLLECT_LTO_WRAPPER=/usr/libexec/gcc/aarch64-linux-gnu/13/lto-wrapper OFFLOAD_TARGET_NAMES=nvptx-none OFFLOAD_TARGET_DEFAULT=1 Target: aarch64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 13.2.0-23' --with-bugurl=file:///usr/share/doc/gcc-13/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-13 --program-prefix=aarch64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libquadmath --disable-libquadmath-support --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --enable-fix-cortex-a53-843419 --disable-werror --enable-offload-targets=nvptx-none=/build/reproducible-path/gcc-13-13.2.0/debian/tmp-nvptx/usr --enable-offload-defaulted --without-cuda-driver --enable-checking=release --build=aarch64-linux-gnu --host=aarch64-linux-gnu --target=aarch64-linux-gnu Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 13.2.0 (Debian 13.2.0-23) 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 SSE2 support... Did not detect SSE2 support Attempting to autodetect SSE3 support... Did not detect SSE3 support Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support Attempting to autodetect NEON support... Compiler supports NEON [ 1/12] Cythonizing mdtraj/formats/dcd/dcd.pyx [ 2/12] Cythonizing mdtraj/geometry/drid.pyx [ 3/12] Cythonizing mdtraj/geometry/neighborlist.pyx [ 4/12] Cythonizing mdtraj/geometry/neighbors.pyx [ 5/12] Cythonizing mdtraj/geometry/src/_geometry.pyx [ 6/12] Cythonizing mdtraj/rmsd/_lprmsd.pyx [ 7/12] Cythonizing mdtraj/formats/binpos/binpos.pyx [ 8/12] Cythonizing mdtraj/formats/dtr/dtr.pyx [ 9/12] Cythonizing mdtraj/formats/tng/tng.pyx [10/12] Cythonizing mdtraj/formats/xtc/trr.pyx [11/12] Cythonizing mdtraj/formats/xtc/xtc.pyx [12/12] Cythonizing mdtraj/rmsd/_rmsd.pyx running build running build_py creating /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj copying mdtraj/version.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj copying mdtraj/io.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj copying mdtraj/__init__.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj creating /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils copying mdtraj/utils/zipped.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils copying mdtraj/utils/validation.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils copying mdtraj/utils/unitcell.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils copying mdtraj/utils/six.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils copying mdtraj/utils/singleton.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils copying mdtraj/utils/rotation.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils copying mdtraj/utils/delay_import.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils copying mdtraj/utils/contextmanagers.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils copying mdtraj/utils/__init__.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils creating /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing copying mdtraj/testing/testing.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing copying mdtraj/testing/docstrings.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing copying mdtraj/testing/docscrape.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing copying mdtraj/testing/__init__.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing creating /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/scripts copying mdtraj/scripts/mdinspect.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/scripts copying mdtraj/scripts/mdconvert.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/scripts copying mdtraj/scripts/__init__.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/scripts creating /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/xtcreporter.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/netcdfreporter.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/hdf5reporter.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/dcdreporter.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/basereporter.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/__init__.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters creating /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/nmr copying mdtraj/nmr/shift_wrappers.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/nmr copying mdtraj/nmr/scalar_couplings.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/nmr copying mdtraj/nmr/__init__.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/nmr creating /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/thermodynamic_properties.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/shape.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/sasa.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/rg.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/rdf.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/order.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/internal.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/hbond.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/dssp.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/distance.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/dihedral.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/contact.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/angle.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/alignment.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/__init__.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry creating /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/xyzfile.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/registry.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/psf.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/prmtop.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/pdbx.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/openmmxml.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/netcdf.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/mol2.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/mdcrd.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/lh5.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/lammpstrj.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/hoomdxml.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/hdf5.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/gsd.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/gro.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/arc.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/amberrst.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/__init__.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats creating /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core copying mdtraj/core/trajectory.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core copying mdtraj/core/topology.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core copying mdtraj/core/selection.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core copying mdtraj/core/residue_names.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core copying mdtraj/core/element.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core copying mdtraj/core/__init__.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core creating /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/unit.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/doctests.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/baseunit.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/basedimension.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/unit_operators.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/unit_math.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/unit_definitions.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/standard_dimensions.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/quantity.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/prefix.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/constants.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/mymatrix.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/__init__.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit creating /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb copying mdtraj/formats/pdb/pdbstructure.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb copying mdtraj/formats/pdb/pdbfile.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb copying mdtraj/formats/pdb/__init__.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb creating /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb/data copying mdtraj/formats/pdb/data/residues.xml -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb/data copying mdtraj/formats/pdb/data/pdbNames.xml -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb/data running build_ext building 'mdtraj.formats.xtc' extension creating build creating build/temp.linux-aarch64-cpython-312 creating build/temp.linux-aarch64-cpython-312/mdtraj creating build/temp.linux-aarch64-cpython-312/mdtraj/formats creating build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc creating build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/src aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/src/xdrfile.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_decompress_coord_float': mdtraj/formats/xtc/src/xdrfile.c:788:32: warning: variable 'larger' set but not used [-Wunused-but-set-variable] 788 | int smallnum, smaller, larger, i, is_smaller, run; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c:785:23: warning: variable 'minidx' set but not used [-Wunused-but-set-variable] 785 | int smallidx, minidx, maxidx; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_compress_coord_float': mdtraj/formats/xtc/src/xdrfile.c:1016:13: warning: variable 'errval' set but not used [-Wunused-but-set-variable] 1016 | int errval=1; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_decompress_coord_double': mdtraj/formats/xtc/src/xdrfile.c:1305:32: warning: variable 'larger' set but not used [-Wunused-but-set-variable] 1305 | int smallnum, smaller, larger, i, is_smaller, run; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c:1302:23: warning: variable 'minidx' set but not used [-Wunused-but-set-variable] 1302 | int smallidx, minidx, maxidx; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_compress_coord_double': mdtraj/formats/xtc/src/xdrfile.c:1509:13: warning: variable 'errval' set but not used [-Wunused-but-set-variable] 1509 | int errval=1; | ^~~~~~ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/xtc/src/xdrfile_xtc.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/src/xdrfile_xtc.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/formats/xtc/src/xdrfile_xtc.c: In function 'xtc_coord': mdtraj/formats/xtc/src/xdrfile_xtc.c:66:15: warning: unused variable 'j' [-Wunused-variable] 66 | int i,j,result; | ^ mdtraj/formats/xtc/src/xdrfile_xtc.c:66:13: warning: unused variable 'i' [-Wunused-variable] 66 | int i,j,result; | ^ mdtraj/formats/xtc/src/xdrfile_xtc.c: In function 'read_xtc_nframes': mdtraj/formats/xtc/src/xdrfile_xtc.c:119:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 119 | if (NULL == xd) | ^~ mdtraj/formats/xtc/src/xdrfile_xtc.c:122:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 122 | do { | ^~ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/xtc/xtc.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/xtc.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1940, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/formats/xtc/xtc.c:784: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ In function '__Pyx_PyInt_From_int', inlined from '__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_16_write' at mdtraj/formats/xtc/xtc.c:9850:16: mdtraj/formats/xtc/xtc.c:696:40: warning: '__pyx_v_status' may be used uninitialized [-Wmaybe-uninitialized] 696 | #define PyInt_FromLong PyLong_FromLong | ^ mdtraj/formats/xtc/xtc.c:19348:20: note: in expansion of macro 'PyInt_FromLong' 19348 | return PyInt_FromLong((long) value); | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c: In function '__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_16_write': mdtraj/formats/xtc/xtc.c:9570:7: note: '__pyx_v_status' was declared here 9570 | int __pyx_v_status; | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c: In function '__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_12_read': mdtraj/formats/xtc/xtc.c:7672:17: warning: '__pyx_pybuffernd_framebuffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 7672 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_framebuffer.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6476:21: note: '__pyx_pybuffernd_framebuffer.diminfo[0].shape' was declared here 6476 | __Pyx_LocalBuf_ND __pyx_pybuffernd_framebuffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:7676:17: warning: '__pyx_pybuffernd_framebuffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 7676 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_framebuffer.diminfo[1].shape)) __pyx_t_6 = 1; | ^ mdtraj/formats/xtc/xtc.c:6476:21: note: '__pyx_pybuffernd_framebuffer.diminfo[1].shape' was declared here 6476 | __Pyx_LocalBuf_ND __pyx_pybuffernd_framebuffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8053:23: warning: '__pyx_pybuffernd_box_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8053 | } else if (unlikely(__pyx_t_32 >= __pyx_pybuffernd_box_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6474:21: note: '__pyx_pybuffernd_box_stride.diminfo[0].shape' was declared here 6474 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8057:23: warning: '__pyx_pybuffernd_box_stride.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8057 | } else if (unlikely(__pyx_t_33 >= __pyx_pybuffernd_box_stride.diminfo[1].shape)) __pyx_t_6 = 1; | ^ mdtraj/formats/xtc/xtc.c:6474:21: note: '__pyx_pybuffernd_box_stride.diminfo[1].shape' was declared here 6474 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8061:23: warning: '__pyx_pybuffernd_box_stride.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 8061 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_box_stride.diminfo[2].shape)) __pyx_t_6 = 2; | ^ mdtraj/formats/xtc/xtc.c:6474:21: note: '__pyx_pybuffernd_box_stride.diminfo[2].shape' was declared here 6474 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8099:23: warning: '__pyx_pybuffernd_prec_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8099 | } else if (unlikely(__pyx_t_40 >= __pyx_pybuffernd_prec_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6480:21: note: '__pyx_pybuffernd_prec_stride.diminfo[0].shape' was declared here 6480 | __Pyx_LocalBuf_ND __pyx_pybuffernd_prec_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8023:23: warning: '__pyx_pybuffernd_step_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8023 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_step_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6484:21: note: '__pyx_pybuffernd_step_stride.diminfo[0].shape' was declared here 6484 | __Pyx_LocalBuf_ND __pyx_pybuffernd_step_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8041:23: warning: '__pyx_pybuffernd_time_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8041 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_time_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6488:21: note: '__pyx_pybuffernd_time_stride.diminfo[0].shape' was declared here 6488 | __Pyx_LocalBuf_ND __pyx_pybuffernd_time_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8081:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8081 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_xyz_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6492:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[0].shape' was declared here 6492 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8085:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8085 | } else if (unlikely(__pyx_t_38 >= __pyx_pybuffernd_xyz_stride.diminfo[1].shape)) __pyx_t_6 = 1; | ^ mdtraj/formats/xtc/xtc.c:6492:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[1].shape' was declared here 6492 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8089:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 8089 | } else if (unlikely(__pyx_t_39 >= __pyx_pybuffernd_xyz_stride.diminfo[2].shape)) __pyx_t_6 = 2; | ^ mdtraj/formats/xtc/xtc.c:6492:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[2].shape' was declared here 6492 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/src/xdrfile_xtc.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/xtc.o -L/usr/lib/aarch64-linux-gnu -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/xtc.cpython-312-aarch64-linux-gnu.so building 'mdtraj.formats.trr' extension aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/src/xdrfile.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_decompress_coord_float': mdtraj/formats/xtc/src/xdrfile.c:788:32: warning: variable 'larger' set but not used [-Wunused-but-set-variable] 788 | int smallnum, smaller, larger, i, is_smaller, run; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c:785:23: warning: variable 'minidx' set but not used [-Wunused-but-set-variable] 785 | int smallidx, minidx, maxidx; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_compress_coord_float': mdtraj/formats/xtc/src/xdrfile.c:1016:13: warning: variable 'errval' set but not used [-Wunused-but-set-variable] 1016 | int errval=1; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_decompress_coord_double': mdtraj/formats/xtc/src/xdrfile.c:1305:32: warning: variable 'larger' set but not used [-Wunused-but-set-variable] 1305 | int smallnum, smaller, larger, i, is_smaller, run; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c:1302:23: warning: variable 'minidx' set but not used [-Wunused-but-set-variable] 1302 | int smallidx, minidx, maxidx; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_compress_coord_double': mdtraj/formats/xtc/src/xdrfile.c:1509:13: warning: variable 'errval' set but not used [-Wunused-but-set-variable] 1509 | int errval=1; | ^~~~~~ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/xtc/src/xdrfile_trr.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/src/xdrfile_trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/xtc/trr.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1940, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/formats/xtc/trr.c:784: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ In function '__Pyx_PyInt_From_int', inlined from '__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_18_write' at mdtraj/formats/xtc/trr.c:11623:16: mdtraj/formats/xtc/trr.c:696:40: warning: '__pyx_v_status' may be used uninitialized [-Wmaybe-uninitialized] 696 | #define PyInt_FromLong PyLong_FromLong | ^ mdtraj/formats/xtc/trr.c:21046:20: note: in expansion of macro 'PyInt_FromLong' 21046 | return PyInt_FromLong((long) value); | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c: In function '__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_18_write': mdtraj/formats/xtc/trr.c:11096:7: note: '__pyx_v_status' was declared here 11096 | int __pyx_v_status; | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c: In function '__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_14_read': mdtraj/formats/xtc/trr.c:8671:19: warning: '__pyx_pybuffernd_forces_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8671 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_forces_buffer.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/trr.c:6988:21: note: '__pyx_pybuffernd_forces_buffer.diminfo[0].shape' was declared here 6988 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8675:19: warning: '__pyx_pybuffernd_forces_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8675 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_forces_buffer.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:6988:21: note: '__pyx_pybuffernd_forces_buffer.diminfo[1].shape' was declared here 6988 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8619:19: warning: '__pyx_pybuffernd_vel_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8619 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_vel_buffer.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/trr.c:7004:21: note: '__pyx_pybuffernd_vel_buffer.diminfo[0].shape' was declared here 7004 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8623:19: warning: '__pyx_pybuffernd_vel_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8623 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_vel_buffer.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:7004:21: note: '__pyx_pybuffernd_vel_buffer.diminfo[1].shape' was declared here 7004 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8778:17: warning: '__pyx_pybuffernd_xyz_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8778 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_xyz_buffer.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/trr.c:7008:21: note: '__pyx_pybuffernd_xyz_buffer.diminfo[0].shape' was declared here 7008 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8782:17: warning: '__pyx_pybuffernd_xyz_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8782 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_xyz_buffer.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:7008:21: note: '__pyx_pybuffernd_xyz_buffer.diminfo[1].shape' was declared here 7008 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8384:19: warning: '__pyx_pybuffernd_vel.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8384 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_vel.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/trr.c:7002:21: note: '__pyx_pybuffernd_vel.diminfo[0].shape' was declared here 7002 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:1935:90: warning: '__pyx_pybuffernd_vel.diminfo[0].strides' may be used uninitialized [-Wmaybe-uninitialized] 1935 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) | ^ mdtraj/formats/xtc/trr.c:8397:42: note: in expansion of macro '__Pyx_BufPtrCContig3d' 8397 | __pyx_v_frame_vel = ((rvec *)(&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_vel.rcbuffer->pybuffer.buf, __pyx_t_29, __pyx_pybuffernd_vel.diminfo[0].strides, __pyx_t_30, __pyx_pybuffernd_vel.diminfo[1].strides, __pyx_t_31, __pyx_pybuffernd_vel.diminfo[2].strides)))); | ^~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:7002:21: note: '__pyx_pybuffernd_vel.diminfo[0].strides' was declared here 7002 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8388:19: warning: '__pyx_pybuffernd_vel.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8388 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_vel.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:7002:21: note: '__pyx_pybuffernd_vel.diminfo[1].shape' was declared here 7002 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8392:19: warning: '__pyx_pybuffernd_vel.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 8392 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_vel.diminfo[2].shape)) __pyx_t_5 = 2; | ^ mdtraj/formats/xtc/trr.c:7002:21: note: '__pyx_pybuffernd_vel.diminfo[2].shape' was declared here 7002 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8441:19: warning: '__pyx_pybuffernd_forces.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8441 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_forces.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/trr.c:6986:21: note: '__pyx_pybuffernd_forces.diminfo[0].shape' was declared here 6986 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:1935:90: warning: '__pyx_pybuffernd_forces.diminfo[0].strides' may be used uninitialized [-Wmaybe-uninitialized] 1935 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) | ^ mdtraj/formats/xtc/trr.c:8454:45: note: in expansion of macro '__Pyx_BufPtrCContig3d' 8454 | __pyx_v_frame_forces = ((rvec *)(&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_forces.rcbuffer->pybuffer.buf, __pyx_t_29, __pyx_pybuffernd_forces.diminfo[0].strides, __pyx_t_31, __pyx_pybuffernd_forces.diminfo[1].strides, __pyx_t_30, __pyx_pybuffernd_forces.diminfo[2].strides)))); | ^~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:6986:21: note: '__pyx_pybuffernd_forces.diminfo[0].strides' was declared here 6986 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8445:19: warning: '__pyx_pybuffernd_forces.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8445 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_forces.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:6986:21: note: '__pyx_pybuffernd_forces.diminfo[1].shape' was declared here 6986 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8449:19: warning: '__pyx_pybuffernd_forces.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 8449 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_forces.diminfo[2].shape)) __pyx_t_5 = 2; | ^ mdtraj/formats/xtc/trr.c:6986:21: note: '__pyx_pybuffernd_forces.diminfo[2].shape' was declared here 6986 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/src/xdrfile_trr.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/trr.o -L/usr/lib/aarch64-linux-gnu -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/trr.cpython-312-aarch64-linux-gnu.so building 'mdtraj.formats.tng' extension creating build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng creating build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src creating build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression creating build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/lib aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/tng/src/compression/bwlzh.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/bwlzh.o aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/tng/src/compression/bwt.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/bwt.o aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/tng/src/compression/coder.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/coder.o aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/tng/src/compression/dict.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/dict.o aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/tng/src/compression/fixpoint.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/fixpoint.o aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/tng/src/compression/huffman.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/huffman.o aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/tng/src/compression/huffmem.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/huffmem.o aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/tng/src/compression/lz77.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/lz77.o aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/tng/src/compression/merge_sort.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/merge_sort.o aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/tng/src/compression/mtf.c -o build/temp.linux-aarch64-cpython-312/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) | ^~ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/tng/src/compression/rle.c -o build/temp.linux-aarch64-cpython-312/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]) | ^~ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/tng/src/compression/tng_compress.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/tng_compress.o aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/tng/src/compression/vals16.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/vals16.o aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/tng/src/compression/warnmalloc.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/warnmalloc.o aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/tng/src/compression/widemuldiv.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/widemuldiv.o aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/tng/src/compression/xtc2.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/xtc2.o aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/tng/src/compression/xtc3.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/xtc3.o aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/tng/src/lib/md5.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/lib/md5.o aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/tng/src/lib/tng_io.c -o build/temp.linux-aarch64-cpython-312/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 = | ^ mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_gen_data_block_add': mdtraj/formats/tng/src/lib/tng_io.c:12613:9: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-truncation] 12613 | strncpy(data->block_name, block_name, strlen(block_name) + 1); | ^ 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); | ^~~~~~~~~~~~~~~~~~ In function 'tng_file_output_numerical', inlined from 'tng_data_block_write.isra' at mdtraj/formats/tng/src/lib/tng_io.c:5969:12: mdtraj/formats/tng/src/lib/tng_io.c:759:22: warning: 'n_particles' may be used uninitialized [-Wmaybe-uninitialized] 759 | temp_i64 = *((int64_t *)src); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_data_block_write.isra': 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; | ^~~~~~~~~~~ In function 'tng_file_output_numerical', inlined from 'tng_data_block_write.isra' at mdtraj/formats/tng/src/lib/tng_io.c:5962:12: mdtraj/formats/tng/src/lib/tng_io.c:759:22: warning: 'num_first_particle' may be used uninitialized [-Wmaybe-uninitialized] 759 | temp_i64 = *((int64_t *)src); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_data_block_write.isra': mdtraj/formats/tng/src/lib/tng_io.c:5684:26: note: 'num_first_particle' was declared here 5684 | int64_t n_particles, num_first_particle, n_frames, stride_length; | ^~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/tng/tng.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/tng.o In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1940, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/formats/tng/tng.c:810: /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:3706:104: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3706 | __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:3761:88: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3761 | __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:3793:90: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3793 | __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:3825:95: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3825 | __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:3895:113: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3895 | __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:3939:77: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3939 | __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:4735:106: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 4735 | __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:4780:108: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 4780 | __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:4887:115: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 4887 | __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:4917:105: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 4917 | __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:5045:105: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 5045 | __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:5646:126: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 5646 | __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:6056:152: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 6056 | __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:6324:108: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 6324 | __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:6426:304: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 6426 | __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:8918:94: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 8918 | __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:8950:75: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 8950 | __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:8982:81: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 8982 | __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:9305:77: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 9305 | __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:9496:372: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 9496 | __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:9548:378: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 9548 | __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:9610:89: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 9610 | __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); | ^~ aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/bwlzh.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/bwt.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/coder.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/dict.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/fixpoint.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/huffman.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/huffmem.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/lz77.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/merge_sort.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/mtf.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/rle.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/tng_compress.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/vals16.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/warnmalloc.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/widemuldiv.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/xtc2.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/xtc3.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/lib/md5.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/lib/tng_io.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/tng.o -L/usr/lib -L/usr/lib/aarch64-linux-gnu -lz -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/tng.cpython-312-aarch64-linux-gnu.so building 'mdtraj.formats.dcd' extension creating build/temp.linux-aarch64-cpython-312/mdtraj/formats/dcd creating build/temp.linux-aarch64-cpython-312/mdtraj/formats/dcd/src aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/dcd/dcd.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/dcd/dcd.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1940, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/formats/dcd/dcd.c:782: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ In function '__Pyx_PyInt_From_int', inlined from '__pyx_pf_6mdtraj_7formats_3dcd_17DCDTrajectoryFile_20read' at mdtraj/formats/dcd/dcd.c:6646:17: mdtraj/formats/dcd/dcd.c:694:40: warning: '__pyx_v_i' may be used uninitialized [-Wmaybe-uninitialized] 694 | #define PyInt_FromLong PyLong_FromLong | ^ mdtraj/formats/dcd/dcd.c:13600:20: note: in expansion of macro 'PyInt_FromLong' 13600 | return PyInt_FromLong((long) value); | ^~~~~~~~~~~~~~ mdtraj/formats/dcd/dcd.c: In function '__pyx_pf_6mdtraj_7formats_3dcd_17DCDTrajectoryFile_20read': mdtraj/formats/dcd/dcd.c:5465:7: note: '__pyx_v_i' was declared here 5465 | int __pyx_v_i; | ^~~~~~~~~ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/dcd/src/dcdplugin.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/dcd/src/dcdplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/mdtraj/formats/dcd/dcd.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/dcd/src/dcdplugin.o -L/usr/lib/aarch64-linux-gnu -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/dcd.cpython-312-aarch64-linux-gnu.so building 'mdtraj.formats.binpos' extension creating build/temp.linux-aarch64-cpython-312/mdtraj/formats/binpos creating build/temp.linux-aarch64-cpython-312/mdtraj/formats/binpos/src aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/binpos/binpos.c -o build/temp.linux-aarch64-cpython-312/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:1940, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/formats/binpos/binpos.c:782: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ In function '__pyx_pf_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_8_read', inlined from '__pyx_pw_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_9_read' at mdtraj/formats/binpos/binpos.c:4994:13: mdtraj/formats/binpos/binpos.c:5526:6: warning: '__pyx_v_status' may be used uninitialized [-Wmaybe-uninitialized] 5526 | if (__pyx_t_2) { | ^ mdtraj/formats/binpos/binpos.c: In function '__pyx_pw_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_9_read': mdtraj/formats/binpos/binpos.c:5006:7: note: '__pyx_v_status' was declared here 5006 | int __pyx_v_status; | ^~~~~~~~~~~~~~ In function '__Pyx_PyInt_From_int', inlined from '__pyx_pf_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_8_read' at mdtraj/formats/binpos/binpos.c:5536:17, inlined from '__pyx_pw_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_9_read' at mdtraj/formats/binpos/binpos.c:4994:13: mdtraj/formats/binpos/binpos.c:694:40: warning: '__pyx_v_i' may be used uninitialized [-Wmaybe-uninitialized] 694 | #define PyInt_FromLong PyLong_FromLong | ^ mdtraj/formats/binpos/binpos.c:13100:20: note: in expansion of macro 'PyInt_FromLong' 13100 | return PyInt_FromLong((long) value); | ^~~~~~~~~~~~~~ mdtraj/formats/binpos/binpos.c: In function '__pyx_pw_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_9_read': mdtraj/formats/binpos/binpos.c:5003:7: note: '__pyx_v_i' was declared here 5003 | int __pyx_v_i; | ^~~~~~~~~ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/binpos/src/binposplugin.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/binpos/src/binposplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/formats/binpos/src/binposplugin.c: In function 'open_binpos_read': mdtraj/formats/binpos/src/binposplugin.c:59:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 59 | fread(magicchar,sizeof(char),4,fd); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/binpos/src/binposplugin.c:69:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 69 | fread(&igarb,sizeof(int),1,fd); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/mdtraj/formats/binpos/binpos.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/binpos/src/binposplugin.o -L/usr/lib/aarch64-linux-gnu -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/binpos.cpython-312-aarch64-linux-gnu.so building 'mdtraj.formats.dtr' extension creating build/temp.linux-aarch64-cpython-312/mdtraj/formats/dtr creating build/temp.linux-aarch64-cpython-312/mdtraj/formats/dtr/src aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/dtr/dtr.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/dtr/dtr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1940, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/formats/dtr/dtr.cpp:803: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/dtr/src/dtrplugin.cxx -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/dtr/src/dtrplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ mdtraj/formats/dtr/src/dtrplugin.cxx: In member function 'bool desres::molfile::Timekeys::init(const std::string&)': mdtraj/formats/dtr/src/dtrplugin.cxx:487:27: warning: format '%d' expects argument of type 'int', but argument 2 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] 487 | printf("size %d framesize %d\n\n", | ~^ | | | int | %ld 488 | keys[i].size(), m_framesize); | ~~~~~~~~~~~~~~ | | | uint64_t {aka long unsigned int} mdtraj/formats/dtr/src/dtrplugin.cxx:487:40: warning: format '%d' expects argument of type 'int', but argument 3 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] 487 | printf("size %d framesize %d\n\n", | ~^ | | | int | %ld 488 | keys[i].size(), m_framesize); | ~~~~~~~~~~~ | | | uint64_t {aka long unsigned int} mdtraj/formats/dtr/src/dtrplugin.cxx: In constructor '{anonymous}::DDException::DDException(const std::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 std::string&, mode_t, int, int)': mdtraj/formats/dtr/src/dtrplugin.cxx:706:23: warning: '%03x' directive writing between 3 and 8 bytes into a region of size 6 [-Wformat-overflow=] 706 | sprintf(sub, "%03x/", i); | ^~~~ mdtraj/formats/dtr/src/dtrplugin.cxx:706:22: note: directive argument in the range [0, 2147483646] 706 | sprintf(sub, "%03x/", i); | ^~~~~~~ In file included from /usr/include/stdio.h:906, from mdtraj/formats/dtr/include/molfile_plugin.h:35, from mdtraj/formats/dtr/include/dtrplugin.hxx:46, from mdtraj/formats/dtr/src/dtrplugin.cxx:42: In function 'int sprintf(char*, const char*, ...)', inlined from 'void DDmkdir(const std::string&, mode_t, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:706:9: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 5 and 10 bytes into a destination of size 6 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ mdtraj/formats/dtr/src/dtrplugin.cxx: In function 'void DDmkdir(const std::string&, mode_t, int, int)': mdtraj/formats/dtr/src/dtrplugin.cxx:714:30: warning: '%03x' directive writing between 3 and 8 bytes into a region of size 6 [-Wformat-overflow=] 714 | sprintf(subsub, "%03x", j); | ^~~~ mdtraj/formats/dtr/src/dtrplugin.cxx:714:29: note: directive argument in the range [0, 2147483646] 714 | sprintf(subsub, "%03x", j); | ^~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'void DDmkdir(const std::string&, mode_t, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:714:13: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 4 and 9 bytes into a destination of size 6 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ mdtraj/formats/dtr/src/dtrplugin.cxx: In function 'std::string framefile(const std::string&, size_t, size_t, int, int)': mdtraj/formats/dtr/src/dtrplugin.cxx:667:35: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=] 667 | sprintf(answer, "%03x/", d1); | ^ In function 'int sprintf(char*, const char*, ...)', inlined from 'std::string DDreldir(const std::string&, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:667:13, inlined from 'std::string framefile(const std::string&, size_t, size_t, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:771:23: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 5 and 10 bytes into a destination of size 9 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ mdtraj/formats/dtr/src/dtrplugin.cxx: In function 'std::string framefile(const std::string&, size_t, size_t, int, int)': mdtraj/formats/dtr/src/dtrplugin.cxx:665:35: warning: '%03x' directive writing between 3 and 8 bytes into a region of size between 0 and 5 [-Wformat-overflow=] 665 | sprintf(answer, "%03x/%03x/", d1, d2); | ^~~~ In function 'std::string DDreldir(const std::string&, int, int)', inlined from 'std::string framefile(const std::string&, size_t, size_t, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:771:23: mdtraj/formats/dtr/src/dtrplugin.cxx:665:29: note: directive argument in the range [0, 2147483646] 665 | sprintf(answer, "%03x/%03x/", d1, d2); | ^~~~~~~~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'std::string DDreldir(const std::string&, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:665:13, inlined from 'std::string framefile(const std::string&, size_t, size_t, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:771:23: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 9 and 19 bytes into a destination of size 9 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/mdtraj/formats/dtr/dtr.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/dtr/src/dtrplugin.o -L/usr/lib/aarch64-linux-gnu -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/dtr.cpython-312-aarch64-linux-gnu.so building 'mdtraj._rmsd' extension creating build/temp.linux-aarch64-cpython-312/mdtraj/rmsd creating build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/_rmsd.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/_rmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/center.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/rotation.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/rotation.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/theobald_rmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/_rmsd.o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/center.o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/rotation.o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/_rmsd.cpython-312-aarch64-linux-gnu.so building 'mdtraj._lprmsd' extension aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/_lprmsd.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/_lprmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1940, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/rmsd/_lprmsd.cpp:812: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/Munkres.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/Munkres.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/center.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/euclidean_permutation.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/euclidean_permutation.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/fancy_index.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/fancy_index.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/rotation.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/rotation.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/theobald_rmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/_lprmsd.o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/Munkres.o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/center.o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/euclidean_permutation.o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/fancy_index.o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/rotation.o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/_lprmsd.cpython-312-aarch64-linux-gnu.so building 'mdtraj.core.lib.libtheobald' extension aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/theobald_rmsd.o -O3 -funroll-loops --std=c++11 cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/center.o -O3 -funroll-loops --std=c++11 cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-gcc-ar rcs /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/lib/libtheobald.a build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/theobald_rmsd.o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/center.o building 'mdtraj.geometry._geometry' extension creating build/temp.linux-aarch64-cpython-312/mdtraj/geometry creating build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/src/_geometry.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/_geometry.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1940, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/geometry/src/_geometry.cpp:814: /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:6129:277: warning: '__pyx_v_offset[1]' may be used uninitialized [-Wmaybe-uninitialized] 6129 | (__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:6035:9: note: '__pyx_v_offset[1]' was declared here 6035 | float __pyx_v_offset[3]; | ^~~~~~~~~~~~~~ mdtraj/geometry/src/_geometry.cpp:6129:277: warning: '__pyx_v_delta[1]' may be used uninitialized [-Wmaybe-uninitialized] 6129 | (__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:6036:9: note: '__pyx_v_delta[1]' was declared here 6036 | float __pyx_v_delta[3]; | ^~~~~~~~~~~~~ mdtraj/geometry/src/_geometry.cpp:6115:224: warning: '__pyx_v_delta[2]' may be used uninitialized [-Wmaybe-uninitialized] 6115 | (__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:6036:9: note: '__pyx_v_delta[2]' was declared here 6036 | float __pyx_v_delta[3]; | ^~~~~~~~~~~~~ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/src/dssp.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/dssp.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/src/geometry.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/geometry.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/src/sasa.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/sasa.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/_geometry.o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/dssp.o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/geometry.o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/sasa.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/_geometry.cpython-312-aarch64-linux-gnu.so building 'mdtraj.geometry.drid' extension aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/drid.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/drid.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/src/dridkernels.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/dridkernels.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/src/moments.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/moments.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/mdtraj/geometry/drid.o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/dridkernels.o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/moments.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/drid.cpython-312-aarch64-linux-gnu.so building 'mdtraj.geometry.neighbors' extension aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/neighbors.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/neighbors.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/src/neighbors.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/neighbors.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/mdtraj/geometry/neighbors.o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/neighbors.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/neighbors.cpython-312-aarch64-linux-gnu.so building 'mdtraj.geometry.neighborlist' extension aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/neighborlist.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/neighborlist.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/src/neighborlist.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/neighborlist.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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:51:53: warning: 'periodicBoxVectors' may be used uninitialized [-Wmaybe-uninitialized] 51 | periodicBoxSize[1] = periodicBoxVectors[1][1]; | ~~~~~~~~~~~~~~~~~~~~~~~^ 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:52:53: warning: 'periodicBoxVectors' may be used uninitialized [-Wmaybe-uninitialized] 52 | periodicBoxSize[2] = periodicBoxVectors[2][2]; | ~~~~~~~~~~~~~~~~~~~~~~~^ 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]; | ^~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/mdtraj/geometry/neighborlist.o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/neighborlist.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/neighborlist.cpython-312-aarch64-linux-gnu.so I: pybuild base:311: /usr/bin/python3 setup.py build Using built-in specs. COLLECT_GCC=/usr/bin/aarch64-linux-gnu-gcc COLLECT_LTO_WRAPPER=/usr/libexec/gcc/aarch64-linux-gnu/13/lto-wrapper OFFLOAD_TARGET_NAMES=nvptx-none OFFLOAD_TARGET_DEFAULT=1 Target: aarch64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 13.2.0-23' --with-bugurl=file:///usr/share/doc/gcc-13/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-13 --program-prefix=aarch64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libquadmath --disable-libquadmath-support --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --enable-fix-cortex-a53-843419 --disable-werror --enable-offload-targets=nvptx-none=/build/reproducible-path/gcc-13-13.2.0/debian/tmp-nvptx/usr --enable-offload-defaulted --without-cuda-driver --enable-checking=release --build=aarch64-linux-gnu --host=aarch64-linux-gnu --target=aarch64-linux-gnu Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 13.2.0 (Debian 13.2.0-23) 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 SSE2 support... Did not detect SSE2 support Attempting to autodetect SSE3 support... Did not detect SSE3 support Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support Attempting to autodetect NEON support... Compiler supports NEON [ 1/12] Cythonizing mdtraj/formats/dcd/dcd.pyx [ 2/12] Cythonizing mdtraj/geometry/drid.pyx [ 3/12] Cythonizing mdtraj/geometry/neighborlist.pyx [ 4/12] Cythonizing mdtraj/geometry/neighbors.pyx [ 5/12] Cythonizing mdtraj/geometry/src/_geometry.pyx [ 6/12] Cythonizing mdtraj/rmsd/_lprmsd.pyx [ 7/12] Cythonizing mdtraj/formats/binpos/binpos.pyx [ 8/12] Cythonizing mdtraj/formats/dtr/dtr.pyx [ 9/12] Cythonizing mdtraj/formats/tng/tng.pyx [10/12] Cythonizing mdtraj/formats/xtc/trr.pyx [11/12] Cythonizing mdtraj/formats/xtc/xtc.pyx [12/12] Cythonizing mdtraj/rmsd/_rmsd.pyx running build running build_py creating /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj copying mdtraj/version.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj copying mdtraj/io.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj copying mdtraj/__init__.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj creating /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils copying mdtraj/utils/zipped.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils copying mdtraj/utils/validation.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils copying mdtraj/utils/unitcell.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils copying mdtraj/utils/six.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils copying mdtraj/utils/singleton.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils copying mdtraj/utils/rotation.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils copying mdtraj/utils/delay_import.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils copying mdtraj/utils/contextmanagers.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils copying mdtraj/utils/__init__.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils creating /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/testing copying mdtraj/testing/testing.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/testing copying mdtraj/testing/docstrings.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/testing copying mdtraj/testing/docscrape.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/testing copying mdtraj/testing/__init__.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/testing creating /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/scripts copying mdtraj/scripts/mdinspect.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/scripts copying mdtraj/scripts/mdconvert.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/scripts copying mdtraj/scripts/__init__.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/scripts creating /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/xtcreporter.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/netcdfreporter.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/hdf5reporter.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/dcdreporter.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/basereporter.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/__init__.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/reporters creating /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/nmr copying mdtraj/nmr/shift_wrappers.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/nmr copying mdtraj/nmr/scalar_couplings.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/nmr copying mdtraj/nmr/__init__.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/nmr creating /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/thermodynamic_properties.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/shape.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/sasa.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/rg.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/rdf.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/order.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/internal.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/hbond.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/dssp.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/distance.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/dihedral.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/contact.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/angle.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/alignment.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/__init__.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry creating /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats copying mdtraj/formats/xyzfile.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats copying mdtraj/formats/registry.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats copying mdtraj/formats/psf.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats copying mdtraj/formats/prmtop.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats copying mdtraj/formats/pdbx.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats copying mdtraj/formats/openmmxml.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats copying mdtraj/formats/netcdf.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats copying mdtraj/formats/mol2.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats copying mdtraj/formats/mdcrd.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats copying mdtraj/formats/lh5.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats copying mdtraj/formats/lammpstrj.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats copying mdtraj/formats/hoomdxml.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats copying mdtraj/formats/hdf5.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats copying mdtraj/formats/gsd.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats copying mdtraj/formats/gro.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats copying mdtraj/formats/arc.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats copying mdtraj/formats/amberrst.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats copying mdtraj/formats/__init__.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats creating /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core copying mdtraj/core/trajectory.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core copying mdtraj/core/topology.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core copying mdtraj/core/selection.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core copying mdtraj/core/residue_names.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core copying mdtraj/core/element.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core copying mdtraj/core/__init__.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core creating /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/unit.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/doctests.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/baseunit.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/basedimension.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/unit_operators.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/unit_math.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/unit_definitions.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/standard_dimensions.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/quantity.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/prefix.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/constants.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/mymatrix.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/__init__.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit creating /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/pdb copying mdtraj/formats/pdb/pdbstructure.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/pdb copying mdtraj/formats/pdb/pdbfile.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/pdb copying mdtraj/formats/pdb/__init__.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/pdb creating /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/pdb/data copying mdtraj/formats/pdb/data/residues.xml -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/pdb/data copying mdtraj/formats/pdb/data/pdbNames.xml -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/pdb/data running build_ext building 'mdtraj.formats.xtc' extension creating build/temp.linux-aarch64-cpython-311 creating build/temp.linux-aarch64-cpython-311/mdtraj creating build/temp.linux-aarch64-cpython-311/mdtraj/formats creating build/temp.linux-aarch64-cpython-311/mdtraj/formats/xtc creating build/temp.linux-aarch64-cpython-311/mdtraj/formats/xtc/src aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.linux-aarch64-cpython-311/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-aarch64-cpython-311/mdtraj/formats/xtc/src/xdrfile.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_decompress_coord_float': mdtraj/formats/xtc/src/xdrfile.c:788:32: warning: variable 'larger' set but not used [-Wunused-but-set-variable] 788 | int smallnum, smaller, larger, i, is_smaller, run; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c:785:23: warning: variable 'minidx' set but not used [-Wunused-but-set-variable] 785 | int smallidx, minidx, maxidx; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_compress_coord_float': mdtraj/formats/xtc/src/xdrfile.c:1016:13: warning: variable 'errval' set but not used [-Wunused-but-set-variable] 1016 | int errval=1; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_decompress_coord_double': mdtraj/formats/xtc/src/xdrfile.c:1305:32: warning: variable 'larger' set but not used [-Wunused-but-set-variable] 1305 | int smallnum, smaller, larger, i, is_smaller, run; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c:1302:23: warning: variable 'minidx' set but not used [-Wunused-but-set-variable] 1302 | int smallidx, minidx, maxidx; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_compress_coord_double': mdtraj/formats/xtc/src/xdrfile.c:1509:13: warning: variable 'errval' set but not used [-Wunused-but-set-variable] 1509 | int errval=1; | ^~~~~~ aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/xtc/src/xdrfile_xtc.c -o build/temp.linux-aarch64-cpython-311/mdtraj/formats/xtc/src/xdrfile_xtc.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/formats/xtc/src/xdrfile_xtc.c: In function 'xtc_coord': mdtraj/formats/xtc/src/xdrfile_xtc.c:66:15: warning: unused variable 'j' [-Wunused-variable] 66 | int i,j,result; | ^ mdtraj/formats/xtc/src/xdrfile_xtc.c:66:13: warning: unused variable 'i' [-Wunused-variable] 66 | int i,j,result; | ^ mdtraj/formats/xtc/src/xdrfile_xtc.c: In function 'read_xtc_nframes': mdtraj/formats/xtc/src/xdrfile_xtc.c:119:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 119 | if (NULL == xd) | ^~ mdtraj/formats/xtc/src/xdrfile_xtc.c:122:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 122 | do { | ^~ aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/xtc/xtc.c -o build/temp.linux-aarch64-cpython-311/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:1940, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/formats/xtc/xtc.c:784: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ In function '__Pyx_PyInt_From_int', inlined from '__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_16_write' at mdtraj/formats/xtc/xtc.c:9850:16: mdtraj/formats/xtc/xtc.c:696:40: warning: '__pyx_v_status' may be used uninitialized [-Wmaybe-uninitialized] 696 | #define PyInt_FromLong PyLong_FromLong | ^ mdtraj/formats/xtc/xtc.c:19348:20: note: in expansion of macro 'PyInt_FromLong' 19348 | return PyInt_FromLong((long) value); | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c: In function '__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_16_write': mdtraj/formats/xtc/xtc.c:9570:7: note: '__pyx_v_status' was declared here 9570 | int __pyx_v_status; | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c: In function '__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_12_read': mdtraj/formats/xtc/xtc.c:7672:17: warning: '__pyx_pybuffernd_framebuffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 7672 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_framebuffer.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6476:21: note: '__pyx_pybuffernd_framebuffer.diminfo[0].shape' was declared here 6476 | __Pyx_LocalBuf_ND __pyx_pybuffernd_framebuffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:7676:17: warning: '__pyx_pybuffernd_framebuffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 7676 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_framebuffer.diminfo[1].shape)) __pyx_t_6 = 1; | ^ mdtraj/formats/xtc/xtc.c:6476:21: note: '__pyx_pybuffernd_framebuffer.diminfo[1].shape' was declared here 6476 | __Pyx_LocalBuf_ND __pyx_pybuffernd_framebuffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8053:23: warning: '__pyx_pybuffernd_box_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8053 | } else if (unlikely(__pyx_t_32 >= __pyx_pybuffernd_box_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6474:21: note: '__pyx_pybuffernd_box_stride.diminfo[0].shape' was declared here 6474 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8057:23: warning: '__pyx_pybuffernd_box_stride.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8057 | } else if (unlikely(__pyx_t_33 >= __pyx_pybuffernd_box_stride.diminfo[1].shape)) __pyx_t_6 = 1; | ^ mdtraj/formats/xtc/xtc.c:6474:21: note: '__pyx_pybuffernd_box_stride.diminfo[1].shape' was declared here 6474 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8061:23: warning: '__pyx_pybuffernd_box_stride.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 8061 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_box_stride.diminfo[2].shape)) __pyx_t_6 = 2; | ^ mdtraj/formats/xtc/xtc.c:6474:21: note: '__pyx_pybuffernd_box_stride.diminfo[2].shape' was declared here 6474 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8099:23: warning: '__pyx_pybuffernd_prec_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8099 | } else if (unlikely(__pyx_t_40 >= __pyx_pybuffernd_prec_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6480:21: note: '__pyx_pybuffernd_prec_stride.diminfo[0].shape' was declared here 6480 | __Pyx_LocalBuf_ND __pyx_pybuffernd_prec_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8023:23: warning: '__pyx_pybuffernd_step_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8023 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_step_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6484:21: note: '__pyx_pybuffernd_step_stride.diminfo[0].shape' was declared here 6484 | __Pyx_LocalBuf_ND __pyx_pybuffernd_step_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8041:23: warning: '__pyx_pybuffernd_time_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8041 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_time_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6488:21: note: '__pyx_pybuffernd_time_stride.diminfo[0].shape' was declared here 6488 | __Pyx_LocalBuf_ND __pyx_pybuffernd_time_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8081:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8081 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_xyz_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6492:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[0].shape' was declared here 6492 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8085:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8085 | } else if (unlikely(__pyx_t_38 >= __pyx_pybuffernd_xyz_stride.diminfo[1].shape)) __pyx_t_6 = 1; | ^ mdtraj/formats/xtc/xtc.c:6492:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[1].shape' was declared here 6492 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8089:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 8089 | } else if (unlikely(__pyx_t_39 >= __pyx_pybuffernd_xyz_stride.diminfo[2].shape)) __pyx_t_6 = 2; | ^ mdtraj/formats/xtc/xtc.c:6492:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[2].shape' was declared here 6492 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-311/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-aarch64-cpython-311/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-aarch64-cpython-311/mdtraj/formats/xtc/src/xdrfile_xtc.o build/temp.linux-aarch64-cpython-311/mdtraj/formats/xtc/xtc.o -L/usr/lib/aarch64-linux-gnu -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/xtc.cpython-311-aarch64-linux-gnu.so building 'mdtraj.formats.trr' extension aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.linux-aarch64-cpython-311/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-aarch64-cpython-311/mdtraj/formats/xtc/src/xdrfile.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_decompress_coord_float': mdtraj/formats/xtc/src/xdrfile.c:788:32: warning: variable 'larger' set but not used [-Wunused-but-set-variable] 788 | int smallnum, smaller, larger, i, is_smaller, run; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c:785:23: warning: variable 'minidx' set but not used [-Wunused-but-set-variable] 785 | int smallidx, minidx, maxidx; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_compress_coord_float': mdtraj/formats/xtc/src/xdrfile.c:1016:13: warning: variable 'errval' set but not used [-Wunused-but-set-variable] 1016 | int errval=1; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_decompress_coord_double': mdtraj/formats/xtc/src/xdrfile.c:1305:32: warning: variable 'larger' set but not used [-Wunused-but-set-variable] 1305 | int smallnum, smaller, larger, i, is_smaller, run; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c:1302:23: warning: variable 'minidx' set but not used [-Wunused-but-set-variable] 1302 | int smallidx, minidx, maxidx; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_compress_coord_double': mdtraj/formats/xtc/src/xdrfile.c:1509:13: warning: variable 'errval' set but not used [-Wunused-but-set-variable] 1509 | int errval=1; | ^~~~~~ aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/xtc/src/xdrfile_trr.c -o build/temp.linux-aarch64-cpython-311/mdtraj/formats/xtc/src/xdrfile_trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/xtc/trr.c -o build/temp.linux-aarch64-cpython-311/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:1940, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/formats/xtc/trr.c:784: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ In function '__Pyx_PyInt_From_int', inlined from '__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_18_write' at mdtraj/formats/xtc/trr.c:11623:16: mdtraj/formats/xtc/trr.c:696:40: warning: '__pyx_v_status' may be used uninitialized [-Wmaybe-uninitialized] 696 | #define PyInt_FromLong PyLong_FromLong | ^ mdtraj/formats/xtc/trr.c:21046:20: note: in expansion of macro 'PyInt_FromLong' 21046 | return PyInt_FromLong((long) value); | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c: In function '__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_18_write': mdtraj/formats/xtc/trr.c:11096:7: note: '__pyx_v_status' was declared here 11096 | int __pyx_v_status; | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c: In function '__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_14_read': mdtraj/formats/xtc/trr.c:8671:19: warning: '__pyx_pybuffernd_forces_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8671 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_forces_buffer.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/trr.c:6988:21: note: '__pyx_pybuffernd_forces_buffer.diminfo[0].shape' was declared here 6988 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8675:19: warning: '__pyx_pybuffernd_forces_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8675 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_forces_buffer.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:6988:21: note: '__pyx_pybuffernd_forces_buffer.diminfo[1].shape' was declared here 6988 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8619:19: warning: '__pyx_pybuffernd_vel_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8619 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_vel_buffer.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/trr.c:7004:21: note: '__pyx_pybuffernd_vel_buffer.diminfo[0].shape' was declared here 7004 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8623:19: warning: '__pyx_pybuffernd_vel_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8623 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_vel_buffer.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:7004:21: note: '__pyx_pybuffernd_vel_buffer.diminfo[1].shape' was declared here 7004 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8778:17: warning: '__pyx_pybuffernd_xyz_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8778 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_xyz_buffer.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/trr.c:7008:21: note: '__pyx_pybuffernd_xyz_buffer.diminfo[0].shape' was declared here 7008 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8782:17: warning: '__pyx_pybuffernd_xyz_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8782 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_xyz_buffer.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:7008:21: note: '__pyx_pybuffernd_xyz_buffer.diminfo[1].shape' was declared here 7008 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8384:19: warning: '__pyx_pybuffernd_vel.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8384 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_vel.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/trr.c:7002:21: note: '__pyx_pybuffernd_vel.diminfo[0].shape' was declared here 7002 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:1935:90: warning: '__pyx_pybuffernd_vel.diminfo[0].strides' may be used uninitialized [-Wmaybe-uninitialized] 1935 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) | ^ mdtraj/formats/xtc/trr.c:8397:42: note: in expansion of macro '__Pyx_BufPtrCContig3d' 8397 | __pyx_v_frame_vel = ((rvec *)(&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_vel.rcbuffer->pybuffer.buf, __pyx_t_29, __pyx_pybuffernd_vel.diminfo[0].strides, __pyx_t_30, __pyx_pybuffernd_vel.diminfo[1].strides, __pyx_t_31, __pyx_pybuffernd_vel.diminfo[2].strides)))); | ^~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:7002:21: note: '__pyx_pybuffernd_vel.diminfo[0].strides' was declared here 7002 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8388:19: warning: '__pyx_pybuffernd_vel.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8388 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_vel.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:7002:21: note: '__pyx_pybuffernd_vel.diminfo[1].shape' was declared here 7002 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8392:19: warning: '__pyx_pybuffernd_vel.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 8392 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_vel.diminfo[2].shape)) __pyx_t_5 = 2; | ^ mdtraj/formats/xtc/trr.c:7002:21: note: '__pyx_pybuffernd_vel.diminfo[2].shape' was declared here 7002 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8441:19: warning: '__pyx_pybuffernd_forces.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8441 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_forces.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/trr.c:6986:21: note: '__pyx_pybuffernd_forces.diminfo[0].shape' was declared here 6986 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:1935:90: warning: '__pyx_pybuffernd_forces.diminfo[0].strides' may be used uninitialized [-Wmaybe-uninitialized] 1935 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) | ^ mdtraj/formats/xtc/trr.c:8454:45: note: in expansion of macro '__Pyx_BufPtrCContig3d' 8454 | __pyx_v_frame_forces = ((rvec *)(&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_forces.rcbuffer->pybuffer.buf, __pyx_t_29, __pyx_pybuffernd_forces.diminfo[0].strides, __pyx_t_31, __pyx_pybuffernd_forces.diminfo[1].strides, __pyx_t_30, __pyx_pybuffernd_forces.diminfo[2].strides)))); | ^~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:6986:21: note: '__pyx_pybuffernd_forces.diminfo[0].strides' was declared here 6986 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8445:19: warning: '__pyx_pybuffernd_forces.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8445 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_forces.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:6986:21: note: '__pyx_pybuffernd_forces.diminfo[1].shape' was declared here 6986 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8449:19: warning: '__pyx_pybuffernd_forces.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 8449 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_forces.diminfo[2].shape)) __pyx_t_5 = 2; | ^ mdtraj/formats/xtc/trr.c:6986:21: note: '__pyx_pybuffernd_forces.diminfo[2].shape' was declared here 6986 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-311/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-aarch64-cpython-311/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-aarch64-cpython-311/mdtraj/formats/xtc/src/xdrfile_trr.o build/temp.linux-aarch64-cpython-311/mdtraj/formats/xtc/trr.o -L/usr/lib/aarch64-linux-gnu -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/trr.cpython-311-aarch64-linux-gnu.so building 'mdtraj.formats.tng' extension creating build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng creating build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src creating build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression creating build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/lib aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/tng/src/compression/bwlzh.c -o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/bwlzh.o aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/tng/src/compression/bwt.c -o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/bwt.o aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/tng/src/compression/coder.c -o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/coder.o aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/tng/src/compression/dict.c -o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/dict.o aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/tng/src/compression/fixpoint.c -o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/fixpoint.o aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/tng/src/compression/huffman.c -o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/huffman.o aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/tng/src/compression/huffmem.c -o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/huffmem.o aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/tng/src/compression/lz77.c -o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/lz77.o aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/tng/src/compression/merge_sort.c -o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/merge_sort.o aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/tng/src/compression/mtf.c -o build/temp.linux-aarch64-cpython-311/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) | ^~ aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/tng/src/compression/rle.c -o build/temp.linux-aarch64-cpython-311/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]) | ^~ aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/tng/src/compression/tng_compress.c -o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/tng_compress.o aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/tng/src/compression/vals16.c -o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/vals16.o aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/tng/src/compression/warnmalloc.c -o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/warnmalloc.o aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/tng/src/compression/widemuldiv.c -o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/widemuldiv.o aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/tng/src/compression/xtc2.c -o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/xtc2.o aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/tng/src/compression/xtc3.c -o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/xtc3.o aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/tng/src/lib/md5.c -o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/lib/md5.o aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/tng/src/lib/tng_io.c -o build/temp.linux-aarch64-cpython-311/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 = | ^ mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_gen_data_block_add': mdtraj/formats/tng/src/lib/tng_io.c:12613:9: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-truncation] 12613 | strncpy(data->block_name, block_name, strlen(block_name) + 1); | ^ 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); | ^~~~~~~~~~~~~~~~~~ In function 'tng_file_output_numerical', inlined from 'tng_data_block_write.isra' at mdtraj/formats/tng/src/lib/tng_io.c:5969:12: mdtraj/formats/tng/src/lib/tng_io.c:759:22: warning: 'n_particles' may be used uninitialized [-Wmaybe-uninitialized] 759 | temp_i64 = *((int64_t *)src); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_data_block_write.isra': 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; | ^~~~~~~~~~~ In function 'tng_file_output_numerical', inlined from 'tng_data_block_write.isra' at mdtraj/formats/tng/src/lib/tng_io.c:5962:12: mdtraj/formats/tng/src/lib/tng_io.c:759:22: warning: 'num_first_particle' may be used uninitialized [-Wmaybe-uninitialized] 759 | temp_i64 = *((int64_t *)src); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_data_block_write.isra': mdtraj/formats/tng/src/lib/tng_io.c:5684:26: note: 'num_first_particle' was declared here 5684 | int64_t n_particles, num_first_particle, n_frames, stride_length; | ^~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/tng/tng.c -o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/tng.o In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1940, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/formats/tng/tng.c:810: /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:3706:104: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3706 | __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:3761:88: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3761 | __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:3793:90: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3793 | __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:3825:95: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3825 | __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:3895:113: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3895 | __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:3939:77: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3939 | __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:4735:106: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 4735 | __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:4780:108: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 4780 | __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:4887:115: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 4887 | __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:4917:105: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 4917 | __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:5045:105: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 5045 | __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:5646:126: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 5646 | __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:6056:152: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 6056 | __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:6324:108: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 6324 | __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:6426:304: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 6426 | __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:8918:94: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 8918 | __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:8950:75: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 8950 | __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:8982:81: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 8982 | __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:9305:77: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 9305 | __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:9496:372: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 9496 | __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:9548:378: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 9548 | __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:9610:89: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 9610 | __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); | ^~ aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/bwlzh.o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/bwt.o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/coder.o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/dict.o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/fixpoint.o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/huffman.o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/huffmem.o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/lz77.o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/merge_sort.o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/mtf.o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/rle.o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/tng_compress.o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/vals16.o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/warnmalloc.o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/widemuldiv.o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/xtc2.o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/xtc3.o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/lib/md5.o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/lib/tng_io.o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/tng.o -L/usr/lib -L/usr/lib/aarch64-linux-gnu -lz -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/tng.cpython-311-aarch64-linux-gnu.so building 'mdtraj.formats.dcd' extension creating build/temp.linux-aarch64-cpython-311/mdtraj/formats/dcd creating build/temp.linux-aarch64-cpython-311/mdtraj/formats/dcd/src aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/dcd/dcd.c -o build/temp.linux-aarch64-cpython-311/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:1940, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/formats/dcd/dcd.c:782: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ In function '__Pyx_PyInt_From_int', inlined from '__pyx_pf_6mdtraj_7formats_3dcd_17DCDTrajectoryFile_20read' at mdtraj/formats/dcd/dcd.c:6646:17: mdtraj/formats/dcd/dcd.c:694:40: warning: '__pyx_v_i' may be used uninitialized [-Wmaybe-uninitialized] 694 | #define PyInt_FromLong PyLong_FromLong | ^ mdtraj/formats/dcd/dcd.c:13600:20: note: in expansion of macro 'PyInt_FromLong' 13600 | return PyInt_FromLong((long) value); | ^~~~~~~~~~~~~~ mdtraj/formats/dcd/dcd.c: In function '__pyx_pf_6mdtraj_7formats_3dcd_17DCDTrajectoryFile_20read': mdtraj/formats/dcd/dcd.c:5465:7: note: '__pyx_v_i' was declared here 5465 | int __pyx_v_i; | ^~~~~~~~~ aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/dcd/src/dcdplugin.c -o build/temp.linux-aarch64-cpython-311/mdtraj/formats/dcd/src/dcdplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-311/mdtraj/formats/dcd/dcd.o build/temp.linux-aarch64-cpython-311/mdtraj/formats/dcd/src/dcdplugin.o -L/usr/lib/aarch64-linux-gnu -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/dcd.cpython-311-aarch64-linux-gnu.so building 'mdtraj.formats.binpos' extension creating build/temp.linux-aarch64-cpython-311/mdtraj/formats/binpos creating build/temp.linux-aarch64-cpython-311/mdtraj/formats/binpos/src aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/binpos/binpos.c -o build/temp.linux-aarch64-cpython-311/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:1940, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/formats/binpos/binpos.c:782: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ In function '__pyx_pf_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_8_read', inlined from '__pyx_pw_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_9_read' at mdtraj/formats/binpos/binpos.c:4994:13: mdtraj/formats/binpos/binpos.c:5526:6: warning: '__pyx_v_status' may be used uninitialized [-Wmaybe-uninitialized] 5526 | if (__pyx_t_2) { | ^ mdtraj/formats/binpos/binpos.c: In function '__pyx_pw_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_9_read': mdtraj/formats/binpos/binpos.c:5006:7: note: '__pyx_v_status' was declared here 5006 | int __pyx_v_status; | ^~~~~~~~~~~~~~ In function '__Pyx_PyInt_From_int', inlined from '__pyx_pf_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_8_read' at mdtraj/formats/binpos/binpos.c:5536:17, inlined from '__pyx_pw_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_9_read' at mdtraj/formats/binpos/binpos.c:4994:13: mdtraj/formats/binpos/binpos.c:694:40: warning: '__pyx_v_i' may be used uninitialized [-Wmaybe-uninitialized] 694 | #define PyInt_FromLong PyLong_FromLong | ^ mdtraj/formats/binpos/binpos.c:13100:20: note: in expansion of macro 'PyInt_FromLong' 13100 | return PyInt_FromLong((long) value); | ^~~~~~~~~~~~~~ mdtraj/formats/binpos/binpos.c: In function '__pyx_pw_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_9_read': mdtraj/formats/binpos/binpos.c:5003:7: note: '__pyx_v_i' was declared here 5003 | int __pyx_v_i; | ^~~~~~~~~ aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/binpos/src/binposplugin.c -o build/temp.linux-aarch64-cpython-311/mdtraj/formats/binpos/src/binposplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/formats/binpos/src/binposplugin.c: In function 'open_binpos_read': mdtraj/formats/binpos/src/binposplugin.c:59:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 59 | fread(magicchar,sizeof(char),4,fd); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/binpos/src/binposplugin.c:69:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 69 | fread(&igarb,sizeof(int),1,fd); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-311/mdtraj/formats/binpos/binpos.o build/temp.linux-aarch64-cpython-311/mdtraj/formats/binpos/src/binposplugin.o -L/usr/lib/aarch64-linux-gnu -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/binpos.cpython-311-aarch64-linux-gnu.so building 'mdtraj.formats.dtr' extension creating build/temp.linux-aarch64-cpython-311/mdtraj/formats/dtr creating build/temp.linux-aarch64-cpython-311/mdtraj/formats/dtr/src aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/dtr/dtr.cpp -o build/temp.linux-aarch64-cpython-311/mdtraj/formats/dtr/dtr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1940, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/formats/dtr/dtr.cpp:803: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/dtr/src/dtrplugin.cxx -o build/temp.linux-aarch64-cpython-311/mdtraj/formats/dtr/src/dtrplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ mdtraj/formats/dtr/src/dtrplugin.cxx: In member function 'bool desres::molfile::Timekeys::init(const std::string&)': mdtraj/formats/dtr/src/dtrplugin.cxx:487:27: warning: format '%d' expects argument of type 'int', but argument 2 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] 487 | printf("size %d framesize %d\n\n", | ~^ | | | int | %ld 488 | keys[i].size(), m_framesize); | ~~~~~~~~~~~~~~ | | | uint64_t {aka long unsigned int} mdtraj/formats/dtr/src/dtrplugin.cxx:487:40: warning: format '%d' expects argument of type 'int', but argument 3 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] 487 | printf("size %d framesize %d\n\n", | ~^ | | | int | %ld 488 | keys[i].size(), m_framesize); | ~~~~~~~~~~~ | | | uint64_t {aka long unsigned int} mdtraj/formats/dtr/src/dtrplugin.cxx: In constructor '{anonymous}::DDException::DDException(const std::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 std::string&, mode_t, int, int)': mdtraj/formats/dtr/src/dtrplugin.cxx:706:23: warning: '%03x' directive writing between 3 and 8 bytes into a region of size 6 [-Wformat-overflow=] 706 | sprintf(sub, "%03x/", i); | ^~~~ mdtraj/formats/dtr/src/dtrplugin.cxx:706:22: note: directive argument in the range [0, 2147483646] 706 | sprintf(sub, "%03x/", i); | ^~~~~~~ In file included from /usr/include/stdio.h:906, from mdtraj/formats/dtr/include/molfile_plugin.h:35, from mdtraj/formats/dtr/include/dtrplugin.hxx:46, from mdtraj/formats/dtr/src/dtrplugin.cxx:42: In function 'int sprintf(char*, const char*, ...)', inlined from 'void DDmkdir(const std::string&, mode_t, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:706:9: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 5 and 10 bytes into a destination of size 6 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ mdtraj/formats/dtr/src/dtrplugin.cxx: In function 'void DDmkdir(const std::string&, mode_t, int, int)': mdtraj/formats/dtr/src/dtrplugin.cxx:714:30: warning: '%03x' directive writing between 3 and 8 bytes into a region of size 6 [-Wformat-overflow=] 714 | sprintf(subsub, "%03x", j); | ^~~~ mdtraj/formats/dtr/src/dtrplugin.cxx:714:29: note: directive argument in the range [0, 2147483646] 714 | sprintf(subsub, "%03x", j); | ^~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'void DDmkdir(const std::string&, mode_t, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:714:13: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 4 and 9 bytes into a destination of size 6 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ mdtraj/formats/dtr/src/dtrplugin.cxx: In function 'std::string framefile(const std::string&, size_t, size_t, int, int)': mdtraj/formats/dtr/src/dtrplugin.cxx:667:35: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=] 667 | sprintf(answer, "%03x/", d1); | ^ In function 'int sprintf(char*, const char*, ...)', inlined from 'std::string DDreldir(const std::string&, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:667:13, inlined from 'std::string framefile(const std::string&, size_t, size_t, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:771:23: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 5 and 10 bytes into a destination of size 9 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ mdtraj/formats/dtr/src/dtrplugin.cxx: In function 'std::string framefile(const std::string&, size_t, size_t, int, int)': mdtraj/formats/dtr/src/dtrplugin.cxx:665:35: warning: '%03x' directive writing between 3 and 8 bytes into a region of size between 0 and 5 [-Wformat-overflow=] 665 | sprintf(answer, "%03x/%03x/", d1, d2); | ^~~~ In function 'std::string DDreldir(const std::string&, int, int)', inlined from 'std::string framefile(const std::string&, size_t, size_t, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:771:23: mdtraj/formats/dtr/src/dtrplugin.cxx:665:29: note: directive argument in the range [0, 2147483646] 665 | sprintf(answer, "%03x/%03x/", d1, d2); | ^~~~~~~~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'std::string DDreldir(const std::string&, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:665:13, inlined from 'std::string framefile(const std::string&, size_t, size_t, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:771:23: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 9 and 19 bytes into a destination of size 9 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-311/mdtraj/formats/dtr/dtr.o build/temp.linux-aarch64-cpython-311/mdtraj/formats/dtr/src/dtrplugin.o -L/usr/lib/aarch64-linux-gnu -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/dtr.cpython-311-aarch64-linux-gnu.so building 'mdtraj._rmsd' extension creating build/temp.linux-aarch64-cpython-311/mdtraj/rmsd creating build/temp.linux-aarch64-cpython-311/mdtraj/rmsd/src aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/rmsd/_rmsd.cpp -o build/temp.linux-aarch64-cpython-311/mdtraj/rmsd/_rmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-aarch64-cpython-311/mdtraj/rmsd/src/center.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/rmsd/src/rotation.cpp -o build/temp.linux-aarch64-cpython-311/mdtraj/rmsd/src/rotation.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-aarch64-cpython-311/mdtraj/rmsd/src/theobald_rmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-311/mdtraj/rmsd/_rmsd.o build/temp.linux-aarch64-cpython-311/mdtraj/rmsd/src/center.o build/temp.linux-aarch64-cpython-311/mdtraj/rmsd/src/rotation.o build/temp.linux-aarch64-cpython-311/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/_rmsd.cpython-311-aarch64-linux-gnu.so building 'mdtraj._lprmsd' extension aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/rmsd/_lprmsd.cpp -o build/temp.linux-aarch64-cpython-311/mdtraj/rmsd/_lprmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1940, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/rmsd/_lprmsd.cpp:812: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/rmsd/src/Munkres.cpp -o build/temp.linux-aarch64-cpython-311/mdtraj/rmsd/src/Munkres.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-aarch64-cpython-311/mdtraj/rmsd/src/center.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/rmsd/src/euclidean_permutation.cpp -o build/temp.linux-aarch64-cpython-311/mdtraj/rmsd/src/euclidean_permutation.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/rmsd/src/fancy_index.cpp -o build/temp.linux-aarch64-cpython-311/mdtraj/rmsd/src/fancy_index.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/rmsd/src/rotation.cpp -o build/temp.linux-aarch64-cpython-311/mdtraj/rmsd/src/rotation.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-aarch64-cpython-311/mdtraj/rmsd/src/theobald_rmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-311/mdtraj/rmsd/_lprmsd.o build/temp.linux-aarch64-cpython-311/mdtraj/rmsd/src/Munkres.o build/temp.linux-aarch64-cpython-311/mdtraj/rmsd/src/center.o build/temp.linux-aarch64-cpython-311/mdtraj/rmsd/src/euclidean_permutation.o build/temp.linux-aarch64-cpython-311/mdtraj/rmsd/src/fancy_index.o build/temp.linux-aarch64-cpython-311/mdtraj/rmsd/src/rotation.o build/temp.linux-aarch64-cpython-311/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/_lprmsd.cpython-311-aarch64-linux-gnu.so building 'mdtraj.core.lib.libtheobald' extension aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-aarch64-cpython-311/mdtraj/rmsd/src/theobald_rmsd.o -O3 -funroll-loops --std=c++11 cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-aarch64-cpython-311/mdtraj/rmsd/src/center.o -O3 -funroll-loops --std=c++11 cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-ar rcs /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core/lib/libtheobald.a build/temp.linux-aarch64-cpython-311/mdtraj/rmsd/src/theobald_rmsd.o build/temp.linux-aarch64-cpython-311/mdtraj/rmsd/src/center.o building 'mdtraj.geometry._geometry' extension creating build/temp.linux-aarch64-cpython-311/mdtraj/geometry creating build/temp.linux-aarch64-cpython-311/mdtraj/geometry/src aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/geometry/src/_geometry.cpp -o build/temp.linux-aarch64-cpython-311/mdtraj/geometry/src/_geometry.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1940, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/geometry/src/_geometry.cpp:814: /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:6129:277: warning: '__pyx_v_offset[1]' may be used uninitialized [-Wmaybe-uninitialized] 6129 | (__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:6035:9: note: '__pyx_v_offset[1]' was declared here 6035 | float __pyx_v_offset[3]; | ^~~~~~~~~~~~~~ mdtraj/geometry/src/_geometry.cpp:6129:277: warning: '__pyx_v_delta[1]' may be used uninitialized [-Wmaybe-uninitialized] 6129 | (__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:6036:9: note: '__pyx_v_delta[1]' was declared here 6036 | float __pyx_v_delta[3]; | ^~~~~~~~~~~~~ mdtraj/geometry/src/_geometry.cpp:6115:224: warning: '__pyx_v_delta[2]' may be used uninitialized [-Wmaybe-uninitialized] 6115 | (__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:6036:9: note: '__pyx_v_delta[2]' was declared here 6036 | float __pyx_v_delta[3]; | ^~~~~~~~~~~~~ aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/geometry/src/dssp.cpp -o build/temp.linux-aarch64-cpython-311/mdtraj/geometry/src/dssp.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/geometry/src/geometry.cpp -o build/temp.linux-aarch64-cpython-311/mdtraj/geometry/src/geometry.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/geometry/src/sasa.cpp -o build/temp.linux-aarch64-cpython-311/mdtraj/geometry/src/sasa.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-311/mdtraj/geometry/src/_geometry.o build/temp.linux-aarch64-cpython-311/mdtraj/geometry/src/dssp.o build/temp.linux-aarch64-cpython-311/mdtraj/geometry/src/geometry.o build/temp.linux-aarch64-cpython-311/mdtraj/geometry/src/sasa.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/_geometry.cpython-311-aarch64-linux-gnu.so building 'mdtraj.geometry.drid' extension aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/geometry/drid.cpp -o build/temp.linux-aarch64-cpython-311/mdtraj/geometry/drid.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/geometry/src/dridkernels.cpp -o build/temp.linux-aarch64-cpython-311/mdtraj/geometry/src/dridkernels.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/geometry/src/moments.cpp -o build/temp.linux-aarch64-cpython-311/mdtraj/geometry/src/moments.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-311/mdtraj/geometry/drid.o build/temp.linux-aarch64-cpython-311/mdtraj/geometry/src/dridkernels.o build/temp.linux-aarch64-cpython-311/mdtraj/geometry/src/moments.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/drid.cpython-311-aarch64-linux-gnu.so building 'mdtraj.geometry.neighbors' extension aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/geometry/neighbors.cpp -o build/temp.linux-aarch64-cpython-311/mdtraj/geometry/neighbors.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/geometry/src/neighbors.cpp -o build/temp.linux-aarch64-cpython-311/mdtraj/geometry/src/neighbors.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-311/mdtraj/geometry/neighbors.o build/temp.linux-aarch64-cpython-311/mdtraj/geometry/src/neighbors.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/neighbors.cpython-311-aarch64-linux-gnu.so building 'mdtraj.geometry.neighborlist' extension aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/geometry/neighborlist.cpp -o build/temp.linux-aarch64-cpython-311/mdtraj/geometry/neighborlist.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/geometry/src/neighborlist.cpp -o build/temp.linux-aarch64-cpython-311/mdtraj/geometry/src/neighborlist.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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:51:53: warning: 'periodicBoxVectors' may be used uninitialized [-Wmaybe-uninitialized] 51 | periodicBoxSize[1] = periodicBoxVectors[1][1]; | ~~~~~~~~~~~~~~~~~~~~~~~^ 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:52:53: warning: 'periodicBoxVectors' may be used uninitialized [-Wmaybe-uninitialized] 52 | periodicBoxSize[2] = periodicBoxVectors[2][2]; | ~~~~~~~~~~~~~~~~~~~~~~~^ 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]; | ^~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-311/mdtraj/geometry/neighborlist.o build/temp.linux-aarch64-cpython-311/mdtraj/geometry/src/neighborlist.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/neighborlist.cpython-311-aarch64-linux-gnu.so cp -a /build/reproducible-path/mdtraj-1.9.9/examples /build/reproducible-path/mdtraj-1.9.9/examples.orig mkdir -p /build/reproducible-path/mdtraj-1.9.9/build/html/examples/iterload ln -s /build/reproducible-path/mdtraj-1.9.9/examples/data /build/reproducible-path/mdtraj-1.9.9/build/html/examples/iterload/data sed "s|http://www.rcsb.org/pdb/files|/build/reproducible-path/mdtraj-1.9.9/debian/external|g" -i /build/reproducible-path/mdtraj-1.9.9/examples/*.ipynb PYTHONPATH=/build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build \ MPLCONFIGDIR=/build/reproducible-path/mdtraj-1.9.9/build/matplotlib \ make -C docs BUILDDIR=/build/reproducible-path/mdtraj-1.9.9/build html make[2]: Entering directory '/build/reproducible-path/mdtraj-1.9.9/docs' sphinx-build -b html -d /build/reproducible-path/mdtraj-1.9.9/build/doctrees . /build/reproducible-path/mdtraj-1.9.9/build/html Running Sphinx v7.2.6 [autosummary] generating autosummary for: analysis.rst, api/reporters.rst, api/trajectory_files.rst, api/utils.rst, atom_selection.rst, building_docs.rst, examples/atom-selection.rst, examples/centroids.rst, examples/clustering.rst, examples/hbonds.rst, ..., examples/solvent-accessible-surface-area.rst, examples/two-pass-clustering.rst, faq.rst, hdf5_format.rst, index.rst, installation.rst, load_functions.rst, mdconvert.rst, new_to_python.rst, whatsnew.rst [autosummary] generating autosummary for: /build/reproducible-path/mdtraj-1.9.9/docs/api/generated/mdtraj.Topology.rst, /build/reproducible-path/mdtraj-1.9.9/docs/api/generated/mdtraj.Trajectory.rst, /build/reproducible-path/mdtraj-1.9.9/docs/api/generated/mdtraj.Trajectory.superpose.rst, /build/reproducible-path/mdtraj-1.9.9/docs/api/generated/mdtraj.acylindricity.rst, /build/reproducible-path/mdtraj-1.9.9/docs/api/generated/mdtraj.asphericity.rst, /build/reproducible-path/mdtraj-1.9.9/docs/api/generated/mdtraj.baker_hubbard.rst, /build/reproducible-path/mdtraj-1.9.9/docs/api/generated/mdtraj.chemical_shifts_ppm.rst, /build/reproducible-path/mdtraj-1.9.9/docs/api/generated/mdtraj.chemical_shifts_shiftx2.rst, /build/reproducible-path/mdtraj-1.9.9/docs/api/generated/mdtraj.chemical_shifts_spartaplus.rst, /build/reproducible-path/mdtraj-1.9.9/docs/api/generated/mdtraj.compute_J3_HN_C.rst, ..., /build/reproducible-path/mdtraj-1.9.9/docs/api/generated/mdtraj.utils.check_random_state.rst, /build/reproducible-path/mdtraj-1.9.9/docs/api/generated/mdtraj.utils.ensure_type.rst, /build/reproducible-path/mdtraj-1.9.9/docs/api/generated/mdtraj.utils.ilen.rst, /build/reproducible-path/mdtraj-1.9.9/docs/api/generated/mdtraj.utils.import_.rst, /build/reproducible-path/mdtraj-1.9.9/docs/api/generated/mdtraj.utils.in_units_of.rst, /build/reproducible-path/mdtraj-1.9.9/docs/api/generated/mdtraj.utils.lengths_and_angles_to_box_vectors.rst, /build/reproducible-path/mdtraj-1.9.9/docs/api/generated/mdtraj.utils.rotation_matrix_from_quaternion.rst, /build/reproducible-path/mdtraj-1.9.9/docs/api/generated/mdtraj.utils.timing.rst, /build/reproducible-path/mdtraj-1.9.9/docs/api/generated/mdtraj.utils.uniform_quaternion.rst, /build/reproducible-path/mdtraj-1.9.9/docs/api/generated/mdtraj.wernet_nilsson.rst building [mo]: targets for 0 po files that are out of date writing output... building [html]: targets for 29 source files that are out of date updating environment: [new config] 127 added, 0 changed, 0 removed reading sources... [ 1%] analysis reading sources... [ 2%] api/generated/mdtraj.Topology /usr/lib/python3/dist-packages/numpydoc/docscrape.py:455: UserWarning: potentially wrong underline length... Returns ---------- in Get the indices of biologically-relevant groups by name. ... in the docstring of select_atom_indices in /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core/topology.py. warn(msg) reading sources... [ 2%] api/generated/mdtraj.Trajectory reading sources... [ 3%] api/generated/mdtraj.Trajectory.superpose reading sources... [ 4%] api/generated/mdtraj.acylindricity reading sources... [ 5%] api/generated/mdtraj.asphericity reading sources... [ 6%] 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... [ 8%] api/generated/mdtraj.chemical_shifts_spartaplus reading sources... 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[ 43%] api/generated/mdtraj.geometry.squareform reading sources... [ 43%] api/generated/mdtraj.isothermal_compressability_kappa_T reading sources... [ 44%] api/generated/mdtraj.iterload reading sources... [ 45%] api/generated/mdtraj.join reading sources... [ 46%] 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... [ 49%] api/generated/mdtraj.load_dcd reading sources... [ 50%] api/generated/mdtraj.load_dtr reading sources... [ 50%] api/generated/mdtraj.load_frame reading sources... [ 51%] api/generated/mdtraj.load_hdf5 reading sources... [ 52%] api/generated/mdtraj.load_hoomdxml reading sources... [ 53%] api/generated/mdtraj.load_lammpstrj reading sources... [ 54%] api/generated/mdtraj.load_lh5 reading sources... [ 54%] api/generated/mdtraj.load_netcdf reading sources... [ 55%] api/generated/mdtraj.load_pdb reading sources... [ 56%] api/generated/mdtraj.load_prmtop reading sources... [ 57%] 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... [ 60%] api/generated/mdtraj.lprmsd reading sources... [ 61%] api/generated/mdtraj.open reading sources... [ 61%] api/generated/mdtraj.principal_moments reading sources... [ 62%] api/generated/mdtraj.reindex_dataframe_by_atoms reading sources... [ 63%] api/generated/mdtraj.relative_shape_antisotropy reading sources... [ 64%] api/generated/mdtraj.reporters.DCDReporter reading sources... [ 65%] api/generated/mdtraj.reporters.HDF5Reporter reading sources... [ 65%] api/generated/mdtraj.reporters.NetCDFReporter reading sources... [ 66%] api/generated/mdtraj.rmsd reading sources... [ 67%] api/generated/mdtraj.rmsf reading sources... 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[100%] whatsnew /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/shape.py:docstring of mdtraj.geometry.shape.asphericity:9: WARNING: Block quote ends without a blank line; unexpected unindent. /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/contact.py:docstring of mdtraj.geometry.contact.compute_contacts:9: WARNING: Block quote ends without a blank line; unexpected unindent. /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/contact.py:docstring of mdtraj.geometry.contact.compute_contacts:36: ERROR: Unexpected indentation. /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/contact.py:docstring of mdtraj.geometry.contact.compute_contacts:45: WARNING: Block quote ends without a blank line; unexpected unindent. docstring of mdtraj.formats.dtr.load_dtr:7: ERROR: Unexpected indentation. /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_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/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/rotation.py:docstring of mdtraj.utils.rotation.uniform_quaternion:37: ERROR: Error in "rubric" directive: no content permitted. .. rubric:: References .. [R17e8d31e726c-1] K. Shoemake. Uniform random rotations. In D. Kirk, editor, Graphics Gems III, pages 124-132. Academic, New York, 1992. .. [R17e8d31e726c-2] http://planning.cs.uiuc.edu/node198.html /build/reproducible-path/mdtraj-1.9.9/docs/examples/atom-selection.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/atom-selection.ipynb :skip_exceptions: /build/reproducible-path/mdtraj-1.9.9/docs/examples/centroids.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/centroids.ipynb :skip_exceptions: /build/reproducible-path/mdtraj-1.9.9/docs/examples/clustering.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/clustering.ipynb :skip_exceptions: /build/reproducible-path/mdtraj-1.9.9/docs/examples/hbonds.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/hbonds.ipynb :skip_exceptions: /build/reproducible-path/mdtraj-1.9.9/docs/examples/iterload.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/iterload.ipynb :skip_exceptions: /build/reproducible-path/mdtraj-1.9.9/docs/examples/native-contact.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/native-contact.ipynb :skip_exceptions: /build/reproducible-path/mdtraj-1.9.9/docs/examples/nmr.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/nmr.ipynb :skip_exceptions: /build/reproducible-path/mdtraj-1.9.9/docs/examples/openmm.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/simulation-with-openmm.ipynb :skip_exceptions: /build/reproducible-path/mdtraj-1.9.9/docs/examples/pca.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/principal-components.ipynb :skip_exceptions: /build/reproducible-path/mdtraj-1.9.9/docs/examples/ramachandran-plot.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/ramachandran-plot.ipynb :skip_exceptions: /build/reproducible-path/mdtraj-1.9.9/docs/examples/rmsd-benchmark.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/rmsd-benchmark.ipynb :skip_exceptions: /build/reproducible-path/mdtraj-1.9.9/docs/examples/solvent-accessible-surface-area.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/solvent-accessible-surface-area.ipynb :skip_exceptions: /build/reproducible-path/mdtraj-1.9.9/docs/examples/two-pass-clustering.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/two-pass-clustering.ipynb :skip_exceptions: /build/reproducible-path/mdtraj-1.9.9/docs/installation.rst:1: WARNING: malformed hyperlink target. /build/reproducible-path/mdtraj-1.9.9/docs/mdconvert.rst:2: WARNING: Title underline too short. ``mdconvert`` (``mdconvert-mdtraj``) ============= /build/reproducible-path/mdtraj-1.9.9/docs/whatsnew.rst:7: WARNING: Title underline too short. v1.9.9 (July 22, 2023) --------------------- /build/reproducible-path/mdtraj-1.9.9/docs/whatsnew.rst:62: WARNING: Title underline too short. v1.9.7 (November 12, 2021) ----------------------- /build/reproducible-path/mdtraj-1.9.9/docs/whatsnew.rst:62: WARNING: Title underline too short. v1.9.7 (November 12, 2021) ----------------------- looking for now-outdated files... none found pickling environment... done checking consistency... /build/reproducible-path/mdtraj-1.9.9/docs/building_docs.rst: WARNING: document isn't included in any toctree /build/reproducible-path/mdtraj-1.9.9/docs/faq.rst: WARNING: document isn't included in any toctree done preparing documents... done copying assets... copying static files... done copying extra files... done done writing output... 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[ 87%] examples/introduction writing output... [ 87%] examples/iterload writing output... [ 88%] examples/native-contact writing output... [ 89%] examples/nmr writing output... [ 90%] examples/openmm writing output... [ 91%] examples/pca writing output... [ 91%] examples/ramachandran-plot writing output... [ 92%] examples/rmsd-benchmark writing output... [ 93%] examples/solvent-accessible-surface-area writing output... [ 94%] examples/two-pass-clustering writing output... [ 94%] faq writing output... [ 95%] hdf5_format writing output... [ 96%] index writing output... [ 97%] installation writing output... [ 98%] 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 dumping search index in English (code: en)... done dumping object inventory... done build succeeded, 28 warnings. The HTML pages are in ../build/html. Build finished. The HTML pages are in /build/reproducible-path/mdtraj-1.9.9/build/html. make[2]: Leaving directory '/build/reproducible-path/mdtraj-1.9.9/docs' for img in `find /build/reproducible-path/mdtraj-1.9.9/build/html/examples -name *.png`; do \ mv $img /build/reproducible-path/mdtraj-1.9.9/build/html/examples; \ done sed "s|/build/reproducible-path/mdtraj-1.9.9/build/html/examples/|./|g; s|.ipynb|.ipynb.gz|g" -i /build/reproducible-path/mdtraj-1.9.9/build/html/examples/*.html sed "s|/build/reproducible-path/mdtraj-1.9.9/debian/external|http://www.rcsb.org/pdb/files|g" -i /build/reproducible-path/mdtraj-1.9.9/build/html/examples/*.html rm /build/reproducible-path/mdtraj-1.9.9/build/html/examples/iterload/data rm -rf /build/reproducible-path/mdtraj-1.9.9/examples mv /build/reproducible-path/mdtraj-1.9.9/examples.orig /build/reproducible-path/mdtraj-1.9.9/examples make[1]: Leaving directory '/build/reproducible-path/mdtraj-1.9.9' dh_auto_build -O--buildsystem=pybuild -Npython-mdtraj-doc pybuild --build -i python{version} -p "3.12 3.11" I: pybuild base:311: /usr/bin/python3.12 setup.py build Using built-in specs. COLLECT_GCC=/usr/bin/aarch64-linux-gnu-gcc COLLECT_LTO_WRAPPER=/usr/libexec/gcc/aarch64-linux-gnu/13/lto-wrapper OFFLOAD_TARGET_NAMES=nvptx-none OFFLOAD_TARGET_DEFAULT=1 Target: aarch64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 13.2.0-23' --with-bugurl=file:///usr/share/doc/gcc-13/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-13 --program-prefix=aarch64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libquadmath --disable-libquadmath-support --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --enable-fix-cortex-a53-843419 --disable-werror --enable-offload-targets=nvptx-none=/build/reproducible-path/gcc-13-13.2.0/debian/tmp-nvptx/usr --enable-offload-defaulted --without-cuda-driver --enable-checking=release --build=aarch64-linux-gnu --host=aarch64-linux-gnu --target=aarch64-linux-gnu Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 13.2.0 (Debian 13.2.0-23) 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 SSE2 support... Did not detect SSE2 support Attempting to autodetect SSE3 support... Did not detect SSE3 support Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support Attempting to autodetect NEON support... Compiler supports NEON [ 1/12] Cythonizing mdtraj/formats/dcd/dcd.pyx [ 2/12] Cythonizing mdtraj/geometry/drid.pyx [ 3/12] Cythonizing mdtraj/geometry/neighborlist.pyx [ 4/12] Cythonizing mdtraj/geometry/neighbors.pyx [ 5/12] Cythonizing mdtraj/geometry/src/_geometry.pyx [ 6/12] Cythonizing mdtraj/rmsd/_lprmsd.pyx [ 7/12] Cythonizing mdtraj/formats/binpos/binpos.pyx [ 8/12] Cythonizing mdtraj/formats/dtr/dtr.pyx [ 9/12] Cythonizing mdtraj/formats/tng/tng.pyx [10/12] Cythonizing mdtraj/formats/xtc/trr.pyx [11/12] Cythonizing mdtraj/formats/xtc/xtc.pyx [12/12] Cythonizing mdtraj/rmsd/_rmsd.pyx running build running build_py copying mdtraj/version.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj running build_ext building 'mdtraj.formats.xtc' extension aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/src/xdrfile.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_decompress_coord_float': mdtraj/formats/xtc/src/xdrfile.c:788:32: warning: variable 'larger' set but not used [-Wunused-but-set-variable] 788 | int smallnum, smaller, larger, i, is_smaller, run; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c:785:23: warning: variable 'minidx' set but not used [-Wunused-but-set-variable] 785 | int smallidx, minidx, maxidx; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_compress_coord_float': mdtraj/formats/xtc/src/xdrfile.c:1016:13: warning: variable 'errval' set but not used [-Wunused-but-set-variable] 1016 | int errval=1; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_decompress_coord_double': mdtraj/formats/xtc/src/xdrfile.c:1305:32: warning: variable 'larger' set but not used [-Wunused-but-set-variable] 1305 | int smallnum, smaller, larger, i, is_smaller, run; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c:1302:23: warning: variable 'minidx' set but not used [-Wunused-but-set-variable] 1302 | int smallidx, minidx, maxidx; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_compress_coord_double': mdtraj/formats/xtc/src/xdrfile.c:1509:13: warning: variable 'errval' set but not used [-Wunused-but-set-variable] 1509 | int errval=1; | ^~~~~~ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/xtc/src/xdrfile_xtc.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/src/xdrfile_xtc.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/formats/xtc/src/xdrfile_xtc.c: In function 'xtc_coord': mdtraj/formats/xtc/src/xdrfile_xtc.c:66:15: warning: unused variable 'j' [-Wunused-variable] 66 | int i,j,result; | ^ mdtraj/formats/xtc/src/xdrfile_xtc.c:66:13: warning: unused variable 'i' [-Wunused-variable] 66 | int i,j,result; | ^ mdtraj/formats/xtc/src/xdrfile_xtc.c: In function 'read_xtc_nframes': mdtraj/formats/xtc/src/xdrfile_xtc.c:119:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 119 | if (NULL == xd) | ^~ mdtraj/formats/xtc/src/xdrfile_xtc.c:122:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 122 | do { | ^~ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/xtc/xtc.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/xtc.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1940, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/formats/xtc/xtc.c:784: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ In function '__Pyx_PyInt_From_int', inlined from '__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_16_write' at mdtraj/formats/xtc/xtc.c:9850:16: mdtraj/formats/xtc/xtc.c:696:40: warning: '__pyx_v_status' may be used uninitialized [-Wmaybe-uninitialized] 696 | #define PyInt_FromLong PyLong_FromLong | ^ mdtraj/formats/xtc/xtc.c:19348:20: note: in expansion of macro 'PyInt_FromLong' 19348 | return PyInt_FromLong((long) value); | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c: In function '__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_16_write': mdtraj/formats/xtc/xtc.c:9570:7: note: '__pyx_v_status' was declared here 9570 | int __pyx_v_status; | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c: In function '__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_12_read': mdtraj/formats/xtc/xtc.c:7672:17: warning: '__pyx_pybuffernd_framebuffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 7672 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_framebuffer.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6476:21: note: '__pyx_pybuffernd_framebuffer.diminfo[0].shape' was declared here 6476 | __Pyx_LocalBuf_ND __pyx_pybuffernd_framebuffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:7676:17: warning: '__pyx_pybuffernd_framebuffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 7676 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_framebuffer.diminfo[1].shape)) __pyx_t_6 = 1; | ^ mdtraj/formats/xtc/xtc.c:6476:21: note: '__pyx_pybuffernd_framebuffer.diminfo[1].shape' was declared here 6476 | __Pyx_LocalBuf_ND __pyx_pybuffernd_framebuffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8053:23: warning: '__pyx_pybuffernd_box_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8053 | } else if (unlikely(__pyx_t_32 >= __pyx_pybuffernd_box_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6474:21: note: '__pyx_pybuffernd_box_stride.diminfo[0].shape' was declared here 6474 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8057:23: warning: '__pyx_pybuffernd_box_stride.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8057 | } else if (unlikely(__pyx_t_33 >= __pyx_pybuffernd_box_stride.diminfo[1].shape)) __pyx_t_6 = 1; | ^ mdtraj/formats/xtc/xtc.c:6474:21: note: '__pyx_pybuffernd_box_stride.diminfo[1].shape' was declared here 6474 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8061:23: warning: '__pyx_pybuffernd_box_stride.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 8061 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_box_stride.diminfo[2].shape)) __pyx_t_6 = 2; | ^ mdtraj/formats/xtc/xtc.c:6474:21: note: '__pyx_pybuffernd_box_stride.diminfo[2].shape' was declared here 6474 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8099:23: warning: '__pyx_pybuffernd_prec_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8099 | } else if (unlikely(__pyx_t_40 >= __pyx_pybuffernd_prec_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6480:21: note: '__pyx_pybuffernd_prec_stride.diminfo[0].shape' was declared here 6480 | __Pyx_LocalBuf_ND __pyx_pybuffernd_prec_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8023:23: warning: '__pyx_pybuffernd_step_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8023 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_step_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6484:21: note: '__pyx_pybuffernd_step_stride.diminfo[0].shape' was declared here 6484 | __Pyx_LocalBuf_ND __pyx_pybuffernd_step_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8041:23: warning: '__pyx_pybuffernd_time_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8041 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_time_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6488:21: note: '__pyx_pybuffernd_time_stride.diminfo[0].shape' was declared here 6488 | __Pyx_LocalBuf_ND __pyx_pybuffernd_time_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8081:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8081 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_xyz_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6492:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[0].shape' was declared here 6492 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8085:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8085 | } else if (unlikely(__pyx_t_38 >= __pyx_pybuffernd_xyz_stride.diminfo[1].shape)) __pyx_t_6 = 1; | ^ mdtraj/formats/xtc/xtc.c:6492:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[1].shape' was declared here 6492 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8089:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 8089 | } else if (unlikely(__pyx_t_39 >= __pyx_pybuffernd_xyz_stride.diminfo[2].shape)) __pyx_t_6 = 2; | ^ mdtraj/formats/xtc/xtc.c:6492:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[2].shape' was declared here 6492 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/src/xdrfile_xtc.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/xtc.o -L/usr/lib/aarch64-linux-gnu -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/xtc.cpython-312-aarch64-linux-gnu.so building 'mdtraj.formats.trr' extension aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/src/xdrfile.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_decompress_coord_float': mdtraj/formats/xtc/src/xdrfile.c:788:32: warning: variable 'larger' set but not used [-Wunused-but-set-variable] 788 | int smallnum, smaller, larger, i, is_smaller, run; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c:785:23: warning: variable 'minidx' set but not used [-Wunused-but-set-variable] 785 | int smallidx, minidx, maxidx; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_compress_coord_float': mdtraj/formats/xtc/src/xdrfile.c:1016:13: warning: variable 'errval' set but not used [-Wunused-but-set-variable] 1016 | int errval=1; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_decompress_coord_double': mdtraj/formats/xtc/src/xdrfile.c:1305:32: warning: variable 'larger' set but not used [-Wunused-but-set-variable] 1305 | int smallnum, smaller, larger, i, is_smaller, run; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c:1302:23: warning: variable 'minidx' set but not used [-Wunused-but-set-variable] 1302 | int smallidx, minidx, maxidx; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_compress_coord_double': mdtraj/formats/xtc/src/xdrfile.c:1509:13: warning: variable 'errval' set but not used [-Wunused-but-set-variable] 1509 | int errval=1; | ^~~~~~ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/xtc/src/xdrfile_trr.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/src/xdrfile_trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/xtc/trr.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1940, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/formats/xtc/trr.c:784: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ In function '__Pyx_PyInt_From_int', inlined from '__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_18_write' at mdtraj/formats/xtc/trr.c:11623:16: mdtraj/formats/xtc/trr.c:696:40: warning: '__pyx_v_status' may be used uninitialized [-Wmaybe-uninitialized] 696 | #define PyInt_FromLong PyLong_FromLong | ^ mdtraj/formats/xtc/trr.c:21046:20: note: in expansion of macro 'PyInt_FromLong' 21046 | return PyInt_FromLong((long) value); | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c: In function '__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_18_write': mdtraj/formats/xtc/trr.c:11096:7: note: '__pyx_v_status' was declared here 11096 | int __pyx_v_status; | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c: In function '__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_14_read': mdtraj/formats/xtc/trr.c:8671:19: warning: '__pyx_pybuffernd_forces_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8671 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_forces_buffer.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/trr.c:6988:21: note: '__pyx_pybuffernd_forces_buffer.diminfo[0].shape' was declared here 6988 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8675:19: warning: '__pyx_pybuffernd_forces_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8675 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_forces_buffer.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:6988:21: note: '__pyx_pybuffernd_forces_buffer.diminfo[1].shape' was declared here 6988 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8619:19: warning: '__pyx_pybuffernd_vel_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8619 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_vel_buffer.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/trr.c:7004:21: note: '__pyx_pybuffernd_vel_buffer.diminfo[0].shape' was declared here 7004 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8623:19: warning: '__pyx_pybuffernd_vel_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8623 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_vel_buffer.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:7004:21: note: '__pyx_pybuffernd_vel_buffer.diminfo[1].shape' was declared here 7004 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8778:17: warning: '__pyx_pybuffernd_xyz_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8778 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_xyz_buffer.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/trr.c:7008:21: note: '__pyx_pybuffernd_xyz_buffer.diminfo[0].shape' was declared here 7008 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8782:17: warning: '__pyx_pybuffernd_xyz_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8782 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_xyz_buffer.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:7008:21: note: '__pyx_pybuffernd_xyz_buffer.diminfo[1].shape' was declared here 7008 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8384:19: warning: '__pyx_pybuffernd_vel.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8384 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_vel.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/trr.c:7002:21: note: '__pyx_pybuffernd_vel.diminfo[0].shape' was declared here 7002 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:1935:90: warning: '__pyx_pybuffernd_vel.diminfo[0].strides' may be used uninitialized [-Wmaybe-uninitialized] 1935 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) | ^ mdtraj/formats/xtc/trr.c:8397:42: note: in expansion of macro '__Pyx_BufPtrCContig3d' 8397 | __pyx_v_frame_vel = ((rvec *)(&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_vel.rcbuffer->pybuffer.buf, __pyx_t_29, __pyx_pybuffernd_vel.diminfo[0].strides, __pyx_t_30, __pyx_pybuffernd_vel.diminfo[1].strides, __pyx_t_31, __pyx_pybuffernd_vel.diminfo[2].strides)))); | ^~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:7002:21: note: '__pyx_pybuffernd_vel.diminfo[0].strides' was declared here 7002 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8388:19: warning: '__pyx_pybuffernd_vel.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8388 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_vel.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:7002:21: note: '__pyx_pybuffernd_vel.diminfo[1].shape' was declared here 7002 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8392:19: warning: '__pyx_pybuffernd_vel.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 8392 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_vel.diminfo[2].shape)) __pyx_t_5 = 2; | ^ mdtraj/formats/xtc/trr.c:7002:21: note: '__pyx_pybuffernd_vel.diminfo[2].shape' was declared here 7002 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8441:19: warning: '__pyx_pybuffernd_forces.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8441 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_forces.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/trr.c:6986:21: note: '__pyx_pybuffernd_forces.diminfo[0].shape' was declared here 6986 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:1935:90: warning: '__pyx_pybuffernd_forces.diminfo[0].strides' may be used uninitialized [-Wmaybe-uninitialized] 1935 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) | ^ mdtraj/formats/xtc/trr.c:8454:45: note: in expansion of macro '__Pyx_BufPtrCContig3d' 8454 | __pyx_v_frame_forces = ((rvec *)(&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_forces.rcbuffer->pybuffer.buf, __pyx_t_29, __pyx_pybuffernd_forces.diminfo[0].strides, __pyx_t_31, __pyx_pybuffernd_forces.diminfo[1].strides, __pyx_t_30, __pyx_pybuffernd_forces.diminfo[2].strides)))); | ^~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:6986:21: note: '__pyx_pybuffernd_forces.diminfo[0].strides' was declared here 6986 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8445:19: warning: '__pyx_pybuffernd_forces.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8445 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_forces.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:6986:21: note: '__pyx_pybuffernd_forces.diminfo[1].shape' was declared here 6986 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8449:19: warning: '__pyx_pybuffernd_forces.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 8449 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_forces.diminfo[2].shape)) __pyx_t_5 = 2; | ^ mdtraj/formats/xtc/trr.c:6986:21: note: '__pyx_pybuffernd_forces.diminfo[2].shape' was declared here 6986 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/src/xdrfile_trr.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/trr.o -L/usr/lib/aarch64-linux-gnu -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/trr.cpython-312-aarch64-linux-gnu.so building 'mdtraj.formats.tng' extension aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/tng/src/compression/bwlzh.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/bwlzh.o aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/tng/src/compression/bwt.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/bwt.o aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/tng/src/compression/coder.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/coder.o aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/tng/src/compression/dict.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/dict.o aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/tng/src/compression/fixpoint.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/fixpoint.o aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/tng/src/compression/huffman.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/huffman.o aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/tng/src/compression/huffmem.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/huffmem.o aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/tng/src/compression/lz77.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/lz77.o aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/tng/src/compression/merge_sort.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/merge_sort.o aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/tng/src/compression/mtf.c -o build/temp.linux-aarch64-cpython-312/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) | ^~ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/tng/src/compression/rle.c -o build/temp.linux-aarch64-cpython-312/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]) | ^~ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/tng/src/compression/tng_compress.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/tng_compress.o aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/tng/src/compression/vals16.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/vals16.o aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/tng/src/compression/warnmalloc.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/warnmalloc.o aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/tng/src/compression/widemuldiv.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/widemuldiv.o aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/tng/src/compression/xtc2.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/xtc2.o aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/tng/src/compression/xtc3.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/xtc3.o aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/tng/src/lib/md5.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/lib/md5.o aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/tng/src/lib/tng_io.c -o build/temp.linux-aarch64-cpython-312/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 = | ^ mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_gen_data_block_add': mdtraj/formats/tng/src/lib/tng_io.c:12613:9: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-truncation] 12613 | strncpy(data->block_name, block_name, strlen(block_name) + 1); | ^ 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); | ^~~~~~~~~~~~~~~~~~ In function 'tng_file_output_numerical', inlined from 'tng_data_block_write.isra' at mdtraj/formats/tng/src/lib/tng_io.c:5969:12: mdtraj/formats/tng/src/lib/tng_io.c:759:22: warning: 'n_particles' may be used uninitialized [-Wmaybe-uninitialized] 759 | temp_i64 = *((int64_t *)src); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_data_block_write.isra': 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; | ^~~~~~~~~~~ In function 'tng_file_output_numerical', inlined from 'tng_data_block_write.isra' at mdtraj/formats/tng/src/lib/tng_io.c:5962:12: mdtraj/formats/tng/src/lib/tng_io.c:759:22: warning: 'num_first_particle' may be used uninitialized [-Wmaybe-uninitialized] 759 | temp_i64 = *((int64_t *)src); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_data_block_write.isra': mdtraj/formats/tng/src/lib/tng_io.c:5684:26: note: 'num_first_particle' was declared here 5684 | int64_t n_particles, num_first_particle, n_frames, stride_length; | ^~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/tng/tng.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/tng.o In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1940, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/formats/tng/tng.c:810: /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:3706:104: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3706 | __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:3761:88: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3761 | __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:3793:90: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3793 | __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:3825:95: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3825 | __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:3895:113: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3895 | __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:3939:77: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3939 | __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:4735:106: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 4735 | __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:4780:108: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 4780 | __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:4887:115: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 4887 | __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:4917:105: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 4917 | __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:5045:105: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 5045 | __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:5646:126: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 5646 | __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:6056:152: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 6056 | __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:6324:108: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 6324 | __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:6426:304: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 6426 | __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:8918:94: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 8918 | __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:8950:75: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 8950 | __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:8982:81: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 8982 | __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:9305:77: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 9305 | __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:9496:372: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 9496 | __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:9548:378: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 9548 | __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:9610:89: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 9610 | __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); | ^~ aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/bwlzh.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/bwt.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/coder.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/dict.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/fixpoint.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/huffman.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/huffmem.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/lz77.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/merge_sort.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/mtf.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/rle.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/tng_compress.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/vals16.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/warnmalloc.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/widemuldiv.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/xtc2.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/xtc3.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/lib/md5.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/lib/tng_io.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/tng.o -L/usr/lib -L/usr/lib/aarch64-linux-gnu -lz -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/tng.cpython-312-aarch64-linux-gnu.so building 'mdtraj.formats.dcd' extension aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/dcd/dcd.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/dcd/dcd.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1940, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/formats/dcd/dcd.c:782: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ In function '__Pyx_PyInt_From_int', inlined from '__pyx_pf_6mdtraj_7formats_3dcd_17DCDTrajectoryFile_20read' at mdtraj/formats/dcd/dcd.c:6646:17: mdtraj/formats/dcd/dcd.c:694:40: warning: '__pyx_v_i' may be used uninitialized [-Wmaybe-uninitialized] 694 | #define PyInt_FromLong PyLong_FromLong | ^ mdtraj/formats/dcd/dcd.c:13600:20: note: in expansion of macro 'PyInt_FromLong' 13600 | return PyInt_FromLong((long) value); | ^~~~~~~~~~~~~~ mdtraj/formats/dcd/dcd.c: In function '__pyx_pf_6mdtraj_7formats_3dcd_17DCDTrajectoryFile_20read': mdtraj/formats/dcd/dcd.c:5465:7: note: '__pyx_v_i' was declared here 5465 | int __pyx_v_i; | ^~~~~~~~~ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/dcd/src/dcdplugin.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/dcd/src/dcdplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/mdtraj/formats/dcd/dcd.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/dcd/src/dcdplugin.o -L/usr/lib/aarch64-linux-gnu -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/dcd.cpython-312-aarch64-linux-gnu.so building 'mdtraj.formats.binpos' extension aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/binpos/binpos.c -o build/temp.linux-aarch64-cpython-312/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:1940, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/formats/binpos/binpos.c:782: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ In function '__pyx_pf_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_8_read', inlined from '__pyx_pw_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_9_read' at mdtraj/formats/binpos/binpos.c:4994:13: mdtraj/formats/binpos/binpos.c:5526:6: warning: '__pyx_v_status' may be used uninitialized [-Wmaybe-uninitialized] 5526 | if (__pyx_t_2) { | ^ mdtraj/formats/binpos/binpos.c: In function '__pyx_pw_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_9_read': mdtraj/formats/binpos/binpos.c:5006:7: note: '__pyx_v_status' was declared here 5006 | int __pyx_v_status; | ^~~~~~~~~~~~~~ In function '__Pyx_PyInt_From_int', inlined from '__pyx_pf_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_8_read' at mdtraj/formats/binpos/binpos.c:5536:17, inlined from '__pyx_pw_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_9_read' at mdtraj/formats/binpos/binpos.c:4994:13: mdtraj/formats/binpos/binpos.c:694:40: warning: '__pyx_v_i' may be used uninitialized [-Wmaybe-uninitialized] 694 | #define PyInt_FromLong PyLong_FromLong | ^ mdtraj/formats/binpos/binpos.c:13100:20: note: in expansion of macro 'PyInt_FromLong' 13100 | return PyInt_FromLong((long) value); | ^~~~~~~~~~~~~~ mdtraj/formats/binpos/binpos.c: In function '__pyx_pw_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_9_read': mdtraj/formats/binpos/binpos.c:5003:7: note: '__pyx_v_i' was declared here 5003 | int __pyx_v_i; | ^~~~~~~~~ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/binpos/src/binposplugin.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/binpos/src/binposplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/formats/binpos/src/binposplugin.c: In function 'open_binpos_read': mdtraj/formats/binpos/src/binposplugin.c:59:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 59 | fread(magicchar,sizeof(char),4,fd); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/binpos/src/binposplugin.c:69:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 69 | fread(&igarb,sizeof(int),1,fd); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/mdtraj/formats/binpos/binpos.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/binpos/src/binposplugin.o -L/usr/lib/aarch64-linux-gnu -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/binpos.cpython-312-aarch64-linux-gnu.so building 'mdtraj.formats.dtr' extension aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/dtr/dtr.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/dtr/dtr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1940, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/formats/dtr/dtr.cpp:803: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/dtr/src/dtrplugin.cxx -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/dtr/src/dtrplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ mdtraj/formats/dtr/src/dtrplugin.cxx: In member function 'bool desres::molfile::Timekeys::init(const std::string&)': mdtraj/formats/dtr/src/dtrplugin.cxx:487:27: warning: format '%d' expects argument of type 'int', but argument 2 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] 487 | printf("size %d framesize %d\n\n", | ~^ | | | int | %ld 488 | keys[i].size(), m_framesize); | ~~~~~~~~~~~~~~ | | | uint64_t {aka long unsigned int} mdtraj/formats/dtr/src/dtrplugin.cxx:487:40: warning: format '%d' expects argument of type 'int', but argument 3 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] 487 | printf("size %d framesize %d\n\n", | ~^ | | | int | %ld 488 | keys[i].size(), m_framesize); | ~~~~~~~~~~~ | | | uint64_t {aka long unsigned int} mdtraj/formats/dtr/src/dtrplugin.cxx: In constructor '{anonymous}::DDException::DDException(const std::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 std::string&, mode_t, int, int)': mdtraj/formats/dtr/src/dtrplugin.cxx:706:23: warning: '%03x' directive writing between 3 and 8 bytes into a region of size 6 [-Wformat-overflow=] 706 | sprintf(sub, "%03x/", i); | ^~~~ mdtraj/formats/dtr/src/dtrplugin.cxx:706:22: note: directive argument in the range [0, 2147483646] 706 | sprintf(sub, "%03x/", i); | ^~~~~~~ In file included from /usr/include/stdio.h:906, from mdtraj/formats/dtr/include/molfile_plugin.h:35, from mdtraj/formats/dtr/include/dtrplugin.hxx:46, from mdtraj/formats/dtr/src/dtrplugin.cxx:42: In function 'int sprintf(char*, const char*, ...)', inlined from 'void DDmkdir(const std::string&, mode_t, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:706:9: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 5 and 10 bytes into a destination of size 6 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ mdtraj/formats/dtr/src/dtrplugin.cxx: In function 'void DDmkdir(const std::string&, mode_t, int, int)': mdtraj/formats/dtr/src/dtrplugin.cxx:714:30: warning: '%03x' directive writing between 3 and 8 bytes into a region of size 6 [-Wformat-overflow=] 714 | sprintf(subsub, "%03x", j); | ^~~~ mdtraj/formats/dtr/src/dtrplugin.cxx:714:29: note: directive argument in the range [0, 2147483646] 714 | sprintf(subsub, "%03x", j); | ^~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'void DDmkdir(const std::string&, mode_t, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:714:13: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 4 and 9 bytes into a destination of size 6 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ mdtraj/formats/dtr/src/dtrplugin.cxx: In function 'std::string framefile(const std::string&, size_t, size_t, int, int)': mdtraj/formats/dtr/src/dtrplugin.cxx:667:35: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=] 667 | sprintf(answer, "%03x/", d1); | ^ In function 'int sprintf(char*, const char*, ...)', inlined from 'std::string DDreldir(const std::string&, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:667:13, inlined from 'std::string framefile(const std::string&, size_t, size_t, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:771:23: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 5 and 10 bytes into a destination of size 9 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ mdtraj/formats/dtr/src/dtrplugin.cxx: In function 'std::string framefile(const std::string&, size_t, size_t, int, int)': mdtraj/formats/dtr/src/dtrplugin.cxx:665:35: warning: '%03x' directive writing between 3 and 8 bytes into a region of size between 0 and 5 [-Wformat-overflow=] 665 | sprintf(answer, "%03x/%03x/", d1, d2); | ^~~~ In function 'std::string DDreldir(const std::string&, int, int)', inlined from 'std::string framefile(const std::string&, size_t, size_t, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:771:23: mdtraj/formats/dtr/src/dtrplugin.cxx:665:29: note: directive argument in the range [0, 2147483646] 665 | sprintf(answer, "%03x/%03x/", d1, d2); | ^~~~~~~~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'std::string DDreldir(const std::string&, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:665:13, inlined from 'std::string framefile(const std::string&, size_t, size_t, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:771:23: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 9 and 19 bytes into a destination of size 9 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/mdtraj/formats/dtr/dtr.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/dtr/src/dtrplugin.o -L/usr/lib/aarch64-linux-gnu -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/dtr.cpython-312-aarch64-linux-gnu.so building 'mdtraj._rmsd' extension aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/_rmsd.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/_rmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/center.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/rotation.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/rotation.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/theobald_rmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/_rmsd.o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/center.o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/rotation.o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/_rmsd.cpython-312-aarch64-linux-gnu.so building 'mdtraj._lprmsd' extension aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/_lprmsd.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/_lprmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1940, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/rmsd/_lprmsd.cpp:812: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/Munkres.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/Munkres.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/center.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/euclidean_permutation.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/euclidean_permutation.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/fancy_index.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/fancy_index.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/rotation.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/rotation.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/theobald_rmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/_lprmsd.o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/Munkres.o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/center.o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/euclidean_permutation.o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/fancy_index.o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/rotation.o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/_lprmsd.cpython-312-aarch64-linux-gnu.so building 'mdtraj.geometry._geometry' extension aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/src/_geometry.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/_geometry.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1940, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/geometry/src/_geometry.cpp:814: /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:6129:277: warning: '__pyx_v_offset[1]' may be used uninitialized [-Wmaybe-uninitialized] 6129 | (__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:6035:9: note: '__pyx_v_offset[1]' was declared here 6035 | float __pyx_v_offset[3]; | ^~~~~~~~~~~~~~ mdtraj/geometry/src/_geometry.cpp:6129:277: warning: '__pyx_v_delta[1]' may be used uninitialized [-Wmaybe-uninitialized] 6129 | (__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:6036:9: note: '__pyx_v_delta[1]' was declared here 6036 | float __pyx_v_delta[3]; | ^~~~~~~~~~~~~ mdtraj/geometry/src/_geometry.cpp:6115:224: warning: '__pyx_v_delta[2]' may be used uninitialized [-Wmaybe-uninitialized] 6115 | (__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:6036:9: note: '__pyx_v_delta[2]' was declared here 6036 | float __pyx_v_delta[3]; | ^~~~~~~~~~~~~ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/src/dssp.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/dssp.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/src/geometry.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/geometry.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/src/sasa.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/sasa.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/_geometry.o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/dssp.o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/geometry.o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/sasa.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/_geometry.cpython-312-aarch64-linux-gnu.so building 'mdtraj.geometry.drid' extension aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/drid.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/drid.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/src/dridkernels.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/dridkernels.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/src/moments.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/moments.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/mdtraj/geometry/drid.o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/dridkernels.o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/moments.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/drid.cpython-312-aarch64-linux-gnu.so building 'mdtraj.geometry.neighbors' extension aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/neighbors.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/neighbors.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/src/neighbors.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/neighbors.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/mdtraj/geometry/neighbors.o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/neighbors.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/neighbors.cpython-312-aarch64-linux-gnu.so building 'mdtraj.geometry.neighborlist' extension aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/neighborlist.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/neighborlist.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/src/neighborlist.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/neighborlist.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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:51:53: warning: 'periodicBoxVectors' may be used uninitialized [-Wmaybe-uninitialized] 51 | periodicBoxSize[1] = periodicBoxVectors[1][1]; | ~~~~~~~~~~~~~~~~~~~~~~~^ 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:52:53: warning: 'periodicBoxVectors' may be used uninitialized [-Wmaybe-uninitialized] 52 | periodicBoxSize[2] = periodicBoxVectors[2][2]; | ~~~~~~~~~~~~~~~~~~~~~~~^ 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]; | ^~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/mdtraj/geometry/neighborlist.o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/neighborlist.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/neighborlist.cpython-312-aarch64-linux-gnu.so I: pybuild base:311: /usr/bin/python3 setup.py build Using built-in specs. COLLECT_GCC=/usr/bin/aarch64-linux-gnu-gcc COLLECT_LTO_WRAPPER=/usr/libexec/gcc/aarch64-linux-gnu/13/lto-wrapper OFFLOAD_TARGET_NAMES=nvptx-none OFFLOAD_TARGET_DEFAULT=1 Target: aarch64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 13.2.0-23' --with-bugurl=file:///usr/share/doc/gcc-13/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-13 --program-prefix=aarch64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libquadmath --disable-libquadmath-support --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --enable-fix-cortex-a53-843419 --disable-werror --enable-offload-targets=nvptx-none=/build/reproducible-path/gcc-13-13.2.0/debian/tmp-nvptx/usr --enable-offload-defaulted --without-cuda-driver --enable-checking=release --build=aarch64-linux-gnu --host=aarch64-linux-gnu --target=aarch64-linux-gnu Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 13.2.0 (Debian 13.2.0-23) 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 SSE2 support... Did not detect SSE2 support Attempting to autodetect SSE3 support... Did not detect SSE3 support Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support Attempting to autodetect NEON support... Compiler supports NEON [ 1/12] Cythonizing mdtraj/formats/dcd/dcd.pyx [ 2/12] Cythonizing mdtraj/geometry/drid.pyx [ 3/12] Cythonizing mdtraj/geometry/neighborlist.pyx [ 4/12] Cythonizing mdtraj/geometry/neighbors.pyx [ 5/12] Cythonizing mdtraj/geometry/src/_geometry.pyx [ 6/12] Cythonizing mdtraj/rmsd/_lprmsd.pyx [ 7/12] Cythonizing mdtraj/formats/binpos/binpos.pyx [ 8/12] Cythonizing mdtraj/formats/dtr/dtr.pyx [ 9/12] Cythonizing mdtraj/formats/tng/tng.pyx [10/12] Cythonizing mdtraj/formats/xtc/trr.pyx [11/12] Cythonizing mdtraj/formats/xtc/xtc.pyx [12/12] Cythonizing mdtraj/rmsd/_rmsd.pyx running build running build_py copying mdtraj/version.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj running build_ext building 'mdtraj.formats.xtc' extension aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.linux-aarch64-cpython-311/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-aarch64-cpython-311/mdtraj/formats/xtc/src/xdrfile.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_decompress_coord_float': mdtraj/formats/xtc/src/xdrfile.c:788:32: warning: variable 'larger' set but not used [-Wunused-but-set-variable] 788 | int smallnum, smaller, larger, i, is_smaller, run; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c:785:23: warning: variable 'minidx' set but not used [-Wunused-but-set-variable] 785 | int smallidx, minidx, maxidx; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_compress_coord_float': mdtraj/formats/xtc/src/xdrfile.c:1016:13: warning: variable 'errval' set but not used [-Wunused-but-set-variable] 1016 | int errval=1; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_decompress_coord_double': mdtraj/formats/xtc/src/xdrfile.c:1305:32: warning: variable 'larger' set but not used [-Wunused-but-set-variable] 1305 | int smallnum, smaller, larger, i, is_smaller, run; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c:1302:23: warning: variable 'minidx' set but not used [-Wunused-but-set-variable] 1302 | int smallidx, minidx, maxidx; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_compress_coord_double': mdtraj/formats/xtc/src/xdrfile.c:1509:13: warning: variable 'errval' set but not used [-Wunused-but-set-variable] 1509 | int errval=1; | ^~~~~~ aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/xtc/src/xdrfile_xtc.c -o build/temp.linux-aarch64-cpython-311/mdtraj/formats/xtc/src/xdrfile_xtc.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/formats/xtc/src/xdrfile_xtc.c: In function 'xtc_coord': mdtraj/formats/xtc/src/xdrfile_xtc.c:66:15: warning: unused variable 'j' [-Wunused-variable] 66 | int i,j,result; | ^ mdtraj/formats/xtc/src/xdrfile_xtc.c:66:13: warning: unused variable 'i' [-Wunused-variable] 66 | int i,j,result; | ^ mdtraj/formats/xtc/src/xdrfile_xtc.c: In function 'read_xtc_nframes': mdtraj/formats/xtc/src/xdrfile_xtc.c:119:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 119 | if (NULL == xd) | ^~ mdtraj/formats/xtc/src/xdrfile_xtc.c:122:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 122 | do { | ^~ aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/xtc/xtc.c -o build/temp.linux-aarch64-cpython-311/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:1940, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/formats/xtc/xtc.c:784: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ In function '__Pyx_PyInt_From_int', inlined from '__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_16_write' at mdtraj/formats/xtc/xtc.c:9850:16: mdtraj/formats/xtc/xtc.c:696:40: warning: '__pyx_v_status' may be used uninitialized [-Wmaybe-uninitialized] 696 | #define PyInt_FromLong PyLong_FromLong | ^ mdtraj/formats/xtc/xtc.c:19348:20: note: in expansion of macro 'PyInt_FromLong' 19348 | return PyInt_FromLong((long) value); | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c: In function '__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_16_write': mdtraj/formats/xtc/xtc.c:9570:7: note: '__pyx_v_status' was declared here 9570 | int __pyx_v_status; | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c: In function '__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_12_read': mdtraj/formats/xtc/xtc.c:7672:17: warning: '__pyx_pybuffernd_framebuffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 7672 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_framebuffer.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6476:21: note: '__pyx_pybuffernd_framebuffer.diminfo[0].shape' was declared here 6476 | __Pyx_LocalBuf_ND __pyx_pybuffernd_framebuffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:7676:17: warning: '__pyx_pybuffernd_framebuffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 7676 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_framebuffer.diminfo[1].shape)) __pyx_t_6 = 1; | ^ mdtraj/formats/xtc/xtc.c:6476:21: note: '__pyx_pybuffernd_framebuffer.diminfo[1].shape' was declared here 6476 | __Pyx_LocalBuf_ND __pyx_pybuffernd_framebuffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8053:23: warning: '__pyx_pybuffernd_box_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8053 | } else if (unlikely(__pyx_t_32 >= __pyx_pybuffernd_box_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6474:21: note: '__pyx_pybuffernd_box_stride.diminfo[0].shape' was declared here 6474 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8057:23: warning: '__pyx_pybuffernd_box_stride.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8057 | } else if (unlikely(__pyx_t_33 >= __pyx_pybuffernd_box_stride.diminfo[1].shape)) __pyx_t_6 = 1; | ^ mdtraj/formats/xtc/xtc.c:6474:21: note: '__pyx_pybuffernd_box_stride.diminfo[1].shape' was declared here 6474 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8061:23: warning: '__pyx_pybuffernd_box_stride.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 8061 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_box_stride.diminfo[2].shape)) __pyx_t_6 = 2; | ^ mdtraj/formats/xtc/xtc.c:6474:21: note: '__pyx_pybuffernd_box_stride.diminfo[2].shape' was declared here 6474 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8099:23: warning: '__pyx_pybuffernd_prec_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8099 | } else if (unlikely(__pyx_t_40 >= __pyx_pybuffernd_prec_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6480:21: note: '__pyx_pybuffernd_prec_stride.diminfo[0].shape' was declared here 6480 | __Pyx_LocalBuf_ND __pyx_pybuffernd_prec_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8023:23: warning: '__pyx_pybuffernd_step_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8023 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_step_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6484:21: note: '__pyx_pybuffernd_step_stride.diminfo[0].shape' was declared here 6484 | __Pyx_LocalBuf_ND __pyx_pybuffernd_step_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8041:23: warning: '__pyx_pybuffernd_time_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8041 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_time_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6488:21: note: '__pyx_pybuffernd_time_stride.diminfo[0].shape' was declared here 6488 | __Pyx_LocalBuf_ND __pyx_pybuffernd_time_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8081:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8081 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_xyz_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6492:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[0].shape' was declared here 6492 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8085:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8085 | } else if (unlikely(__pyx_t_38 >= __pyx_pybuffernd_xyz_stride.diminfo[1].shape)) __pyx_t_6 = 1; | ^ mdtraj/formats/xtc/xtc.c:6492:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[1].shape' was declared here 6492 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8089:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 8089 | } else if (unlikely(__pyx_t_39 >= __pyx_pybuffernd_xyz_stride.diminfo[2].shape)) __pyx_t_6 = 2; | ^ mdtraj/formats/xtc/xtc.c:6492:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[2].shape' was declared here 6492 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-311/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-aarch64-cpython-311/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-aarch64-cpython-311/mdtraj/formats/xtc/src/xdrfile_xtc.o build/temp.linux-aarch64-cpython-311/mdtraj/formats/xtc/xtc.o -L/usr/lib/aarch64-linux-gnu -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/xtc.cpython-311-aarch64-linux-gnu.so building 'mdtraj.formats.trr' extension aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.linux-aarch64-cpython-311/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-aarch64-cpython-311/mdtraj/formats/xtc/src/xdrfile.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_decompress_coord_float': mdtraj/formats/xtc/src/xdrfile.c:788:32: warning: variable 'larger' set but not used [-Wunused-but-set-variable] 788 | int smallnum, smaller, larger, i, is_smaller, run; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c:785:23: warning: variable 'minidx' set but not used [-Wunused-but-set-variable] 785 | int smallidx, minidx, maxidx; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_compress_coord_float': mdtraj/formats/xtc/src/xdrfile.c:1016:13: warning: variable 'errval' set but not used [-Wunused-but-set-variable] 1016 | int errval=1; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_decompress_coord_double': mdtraj/formats/xtc/src/xdrfile.c:1305:32: warning: variable 'larger' set but not used [-Wunused-but-set-variable] 1305 | int smallnum, smaller, larger, i, is_smaller, run; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c:1302:23: warning: variable 'minidx' set but not used [-Wunused-but-set-variable] 1302 | int smallidx, minidx, maxidx; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_compress_coord_double': mdtraj/formats/xtc/src/xdrfile.c:1509:13: warning: variable 'errval' set but not used [-Wunused-but-set-variable] 1509 | int errval=1; | ^~~~~~ aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/xtc/src/xdrfile_trr.c -o build/temp.linux-aarch64-cpython-311/mdtraj/formats/xtc/src/xdrfile_trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/xtc/trr.c -o build/temp.linux-aarch64-cpython-311/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:1940, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/formats/xtc/trr.c:784: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ In function '__Pyx_PyInt_From_int', inlined from '__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_18_write' at mdtraj/formats/xtc/trr.c:11623:16: mdtraj/formats/xtc/trr.c:696:40: warning: '__pyx_v_status' may be used uninitialized [-Wmaybe-uninitialized] 696 | #define PyInt_FromLong PyLong_FromLong | ^ mdtraj/formats/xtc/trr.c:21046:20: note: in expansion of macro 'PyInt_FromLong' 21046 | return PyInt_FromLong((long) value); | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c: In function '__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_18_write': mdtraj/formats/xtc/trr.c:11096:7: note: '__pyx_v_status' was declared here 11096 | int __pyx_v_status; | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c: In function '__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_14_read': mdtraj/formats/xtc/trr.c:8671:19: warning: '__pyx_pybuffernd_forces_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8671 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_forces_buffer.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/trr.c:6988:21: note: '__pyx_pybuffernd_forces_buffer.diminfo[0].shape' was declared here 6988 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8675:19: warning: '__pyx_pybuffernd_forces_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8675 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_forces_buffer.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:6988:21: note: '__pyx_pybuffernd_forces_buffer.diminfo[1].shape' was declared here 6988 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8619:19: warning: '__pyx_pybuffernd_vel_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8619 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_vel_buffer.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/trr.c:7004:21: note: '__pyx_pybuffernd_vel_buffer.diminfo[0].shape' was declared here 7004 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8623:19: warning: '__pyx_pybuffernd_vel_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8623 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_vel_buffer.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:7004:21: note: '__pyx_pybuffernd_vel_buffer.diminfo[1].shape' was declared here 7004 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8778:17: warning: '__pyx_pybuffernd_xyz_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8778 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_xyz_buffer.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/trr.c:7008:21: note: '__pyx_pybuffernd_xyz_buffer.diminfo[0].shape' was declared here 7008 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8782:17: warning: '__pyx_pybuffernd_xyz_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8782 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_xyz_buffer.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:7008:21: note: '__pyx_pybuffernd_xyz_buffer.diminfo[1].shape' was declared here 7008 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8384:19: warning: '__pyx_pybuffernd_vel.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8384 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_vel.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/trr.c:7002:21: note: '__pyx_pybuffernd_vel.diminfo[0].shape' was declared here 7002 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:1935:90: warning: '__pyx_pybuffernd_vel.diminfo[0].strides' may be used uninitialized [-Wmaybe-uninitialized] 1935 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) | ^ mdtraj/formats/xtc/trr.c:8397:42: note: in expansion of macro '__Pyx_BufPtrCContig3d' 8397 | __pyx_v_frame_vel = ((rvec *)(&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_vel.rcbuffer->pybuffer.buf, __pyx_t_29, __pyx_pybuffernd_vel.diminfo[0].strides, __pyx_t_30, __pyx_pybuffernd_vel.diminfo[1].strides, __pyx_t_31, __pyx_pybuffernd_vel.diminfo[2].strides)))); | ^~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:7002:21: note: '__pyx_pybuffernd_vel.diminfo[0].strides' was declared here 7002 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8388:19: warning: '__pyx_pybuffernd_vel.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8388 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_vel.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:7002:21: note: '__pyx_pybuffernd_vel.diminfo[1].shape' was declared here 7002 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8392:19: warning: '__pyx_pybuffernd_vel.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 8392 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_vel.diminfo[2].shape)) __pyx_t_5 = 2; | ^ mdtraj/formats/xtc/trr.c:7002:21: note: '__pyx_pybuffernd_vel.diminfo[2].shape' was declared here 7002 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8441:19: warning: '__pyx_pybuffernd_forces.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8441 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_forces.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/trr.c:6986:21: note: '__pyx_pybuffernd_forces.diminfo[0].shape' was declared here 6986 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:1935:90: warning: '__pyx_pybuffernd_forces.diminfo[0].strides' may be used uninitialized [-Wmaybe-uninitialized] 1935 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) | ^ mdtraj/formats/xtc/trr.c:8454:45: note: in expansion of macro '__Pyx_BufPtrCContig3d' 8454 | __pyx_v_frame_forces = ((rvec *)(&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_forces.rcbuffer->pybuffer.buf, __pyx_t_29, __pyx_pybuffernd_forces.diminfo[0].strides, __pyx_t_31, __pyx_pybuffernd_forces.diminfo[1].strides, __pyx_t_30, __pyx_pybuffernd_forces.diminfo[2].strides)))); | ^~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:6986:21: note: '__pyx_pybuffernd_forces.diminfo[0].strides' was declared here 6986 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8445:19: warning: '__pyx_pybuffernd_forces.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8445 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_forces.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:6986:21: note: '__pyx_pybuffernd_forces.diminfo[1].shape' was declared here 6986 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8449:19: warning: '__pyx_pybuffernd_forces.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 8449 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_forces.diminfo[2].shape)) __pyx_t_5 = 2; | ^ mdtraj/formats/xtc/trr.c:6986:21: note: '__pyx_pybuffernd_forces.diminfo[2].shape' was declared here 6986 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-311/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-aarch64-cpython-311/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-aarch64-cpython-311/mdtraj/formats/xtc/src/xdrfile_trr.o build/temp.linux-aarch64-cpython-311/mdtraj/formats/xtc/trr.o -L/usr/lib/aarch64-linux-gnu -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/trr.cpython-311-aarch64-linux-gnu.so building 'mdtraj.formats.tng' extension aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/tng/src/compression/bwlzh.c -o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/bwlzh.o aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/tng/src/compression/bwt.c -o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/bwt.o aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/tng/src/compression/coder.c -o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/coder.o aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/tng/src/compression/dict.c -o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/dict.o aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/tng/src/compression/fixpoint.c -o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/fixpoint.o aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/tng/src/compression/huffman.c -o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/huffman.o aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/tng/src/compression/huffmem.c -o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/huffmem.o aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/tng/src/compression/lz77.c -o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/lz77.o aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/tng/src/compression/merge_sort.c -o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/merge_sort.o aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/tng/src/compression/mtf.c -o build/temp.linux-aarch64-cpython-311/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) | ^~ aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/tng/src/compression/rle.c -o build/temp.linux-aarch64-cpython-311/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]) | ^~ aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/tng/src/compression/tng_compress.c -o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/tng_compress.o aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/tng/src/compression/vals16.c -o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/vals16.o aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/tng/src/compression/warnmalloc.c -o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/warnmalloc.o aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/tng/src/compression/widemuldiv.c -o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/widemuldiv.o aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/tng/src/compression/xtc2.c -o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/xtc2.o aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/tng/src/compression/xtc3.c -o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/xtc3.o aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/tng/src/lib/md5.c -o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/lib/md5.o aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/tng/src/lib/tng_io.c -o build/temp.linux-aarch64-cpython-311/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 = | ^ mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_gen_data_block_add': mdtraj/formats/tng/src/lib/tng_io.c:12613:9: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-truncation] 12613 | strncpy(data->block_name, block_name, strlen(block_name) + 1); | ^ 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); | ^~~~~~~~~~~~~~~~~~ In function 'tng_file_output_numerical', inlined from 'tng_data_block_write.isra' at mdtraj/formats/tng/src/lib/tng_io.c:5969:12: mdtraj/formats/tng/src/lib/tng_io.c:759:22: warning: 'n_particles' may be used uninitialized [-Wmaybe-uninitialized] 759 | temp_i64 = *((int64_t *)src); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_data_block_write.isra': 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; | ^~~~~~~~~~~ In function 'tng_file_output_numerical', inlined from 'tng_data_block_write.isra' at mdtraj/formats/tng/src/lib/tng_io.c:5962:12: mdtraj/formats/tng/src/lib/tng_io.c:759:22: warning: 'num_first_particle' may be used uninitialized [-Wmaybe-uninitialized] 759 | temp_i64 = *((int64_t *)src); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_data_block_write.isra': mdtraj/formats/tng/src/lib/tng_io.c:5684:26: note: 'num_first_particle' was declared here 5684 | int64_t n_particles, num_first_particle, n_frames, stride_length; | ^~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/tng/tng.c -o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/tng.o In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1940, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/formats/tng/tng.c:810: /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:3706:104: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3706 | __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:3761:88: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3761 | __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:3793:90: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3793 | __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:3825:95: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3825 | __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:3895:113: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3895 | __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:3939:77: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3939 | __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:4735:106: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 4735 | __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:4780:108: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 4780 | __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:4887:115: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 4887 | __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:4917:105: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 4917 | __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:5045:105: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 5045 | __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:5646:126: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 5646 | __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:6056:152: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 6056 | __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:6324:108: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 6324 | __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:6426:304: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 6426 | __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:8918:94: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 8918 | __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:8950:75: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 8950 | __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:8982:81: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 8982 | __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:9305:77: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 9305 | __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:9496:372: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 9496 | __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:9548:378: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 9548 | __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:9610:89: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 9610 | __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); | ^~ aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/bwlzh.o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/bwt.o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/coder.o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/dict.o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/fixpoint.o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/huffman.o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/huffmem.o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/lz77.o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/merge_sort.o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/mtf.o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/rle.o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/tng_compress.o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/vals16.o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/warnmalloc.o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/widemuldiv.o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/xtc2.o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/xtc3.o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/lib/md5.o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/lib/tng_io.o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/tng.o -L/usr/lib -L/usr/lib/aarch64-linux-gnu -lz -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/tng.cpython-311-aarch64-linux-gnu.so building 'mdtraj.formats.dcd' extension aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/dcd/dcd.c -o build/temp.linux-aarch64-cpython-311/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:1940, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/formats/dcd/dcd.c:782: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ In function '__Pyx_PyInt_From_int', inlined from '__pyx_pf_6mdtraj_7formats_3dcd_17DCDTrajectoryFile_20read' at mdtraj/formats/dcd/dcd.c:6646:17: mdtraj/formats/dcd/dcd.c:694:40: warning: '__pyx_v_i' may be used uninitialized [-Wmaybe-uninitialized] 694 | #define PyInt_FromLong PyLong_FromLong | ^ mdtraj/formats/dcd/dcd.c:13600:20: note: in expansion of macro 'PyInt_FromLong' 13600 | return PyInt_FromLong((long) value); | ^~~~~~~~~~~~~~ mdtraj/formats/dcd/dcd.c: In function '__pyx_pf_6mdtraj_7formats_3dcd_17DCDTrajectoryFile_20read': mdtraj/formats/dcd/dcd.c:5465:7: note: '__pyx_v_i' was declared here 5465 | int __pyx_v_i; | ^~~~~~~~~ aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/dcd/src/dcdplugin.c -o build/temp.linux-aarch64-cpython-311/mdtraj/formats/dcd/src/dcdplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-311/mdtraj/formats/dcd/dcd.o build/temp.linux-aarch64-cpython-311/mdtraj/formats/dcd/src/dcdplugin.o -L/usr/lib/aarch64-linux-gnu -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/dcd.cpython-311-aarch64-linux-gnu.so building 'mdtraj.formats.binpos' extension aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/binpos/binpos.c -o build/temp.linux-aarch64-cpython-311/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:1940, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/formats/binpos/binpos.c:782: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ In function '__pyx_pf_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_8_read', inlined from '__pyx_pw_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_9_read' at mdtraj/formats/binpos/binpos.c:4994:13: mdtraj/formats/binpos/binpos.c:5526:6: warning: '__pyx_v_status' may be used uninitialized [-Wmaybe-uninitialized] 5526 | if (__pyx_t_2) { | ^ mdtraj/formats/binpos/binpos.c: In function '__pyx_pw_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_9_read': mdtraj/formats/binpos/binpos.c:5006:7: note: '__pyx_v_status' was declared here 5006 | int __pyx_v_status; | ^~~~~~~~~~~~~~ In function '__Pyx_PyInt_From_int', inlined from '__pyx_pf_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_8_read' at mdtraj/formats/binpos/binpos.c:5536:17, inlined from '__pyx_pw_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_9_read' at mdtraj/formats/binpos/binpos.c:4994:13: mdtraj/formats/binpos/binpos.c:694:40: warning: '__pyx_v_i' may be used uninitialized [-Wmaybe-uninitialized] 694 | #define PyInt_FromLong PyLong_FromLong | ^ mdtraj/formats/binpos/binpos.c:13100:20: note: in expansion of macro 'PyInt_FromLong' 13100 | return PyInt_FromLong((long) value); | ^~~~~~~~~~~~~~ mdtraj/formats/binpos/binpos.c: In function '__pyx_pw_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_9_read': mdtraj/formats/binpos/binpos.c:5003:7: note: '__pyx_v_i' was declared here 5003 | int __pyx_v_i; | ^~~~~~~~~ aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/binpos/src/binposplugin.c -o build/temp.linux-aarch64-cpython-311/mdtraj/formats/binpos/src/binposplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/formats/binpos/src/binposplugin.c: In function 'open_binpos_read': mdtraj/formats/binpos/src/binposplugin.c:59:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 59 | fread(magicchar,sizeof(char),4,fd); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/binpos/src/binposplugin.c:69:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 69 | fread(&igarb,sizeof(int),1,fd); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-311/mdtraj/formats/binpos/binpos.o build/temp.linux-aarch64-cpython-311/mdtraj/formats/binpos/src/binposplugin.o -L/usr/lib/aarch64-linux-gnu -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/binpos.cpython-311-aarch64-linux-gnu.so building 'mdtraj.formats.dtr' extension aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/dtr/dtr.cpp -o build/temp.linux-aarch64-cpython-311/mdtraj/formats/dtr/dtr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1940, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/formats/dtr/dtr.cpp:803: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/dtr/src/dtrplugin.cxx -o build/temp.linux-aarch64-cpython-311/mdtraj/formats/dtr/src/dtrplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ mdtraj/formats/dtr/src/dtrplugin.cxx: In member function 'bool desres::molfile::Timekeys::init(const std::string&)': mdtraj/formats/dtr/src/dtrplugin.cxx:487:27: warning: format '%d' expects argument of type 'int', but argument 2 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] 487 | printf("size %d framesize %d\n\n", | ~^ | | | int | %ld 488 | keys[i].size(), m_framesize); | ~~~~~~~~~~~~~~ | | | uint64_t {aka long unsigned int} mdtraj/formats/dtr/src/dtrplugin.cxx:487:40: warning: format '%d' expects argument of type 'int', but argument 3 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] 487 | printf("size %d framesize %d\n\n", | ~^ | | | int | %ld 488 | keys[i].size(), m_framesize); | ~~~~~~~~~~~ | | | uint64_t {aka long unsigned int} mdtraj/formats/dtr/src/dtrplugin.cxx: In constructor '{anonymous}::DDException::DDException(const std::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 std::string&, mode_t, int, int)': mdtraj/formats/dtr/src/dtrplugin.cxx:706:23: warning: '%03x' directive writing between 3 and 8 bytes into a region of size 6 [-Wformat-overflow=] 706 | sprintf(sub, "%03x/", i); | ^~~~ mdtraj/formats/dtr/src/dtrplugin.cxx:706:22: note: directive argument in the range [0, 2147483646] 706 | sprintf(sub, "%03x/", i); | ^~~~~~~ In file included from /usr/include/stdio.h:906, from mdtraj/formats/dtr/include/molfile_plugin.h:35, from mdtraj/formats/dtr/include/dtrplugin.hxx:46, from mdtraj/formats/dtr/src/dtrplugin.cxx:42: In function 'int sprintf(char*, const char*, ...)', inlined from 'void DDmkdir(const std::string&, mode_t, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:706:9: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 5 and 10 bytes into a destination of size 6 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ mdtraj/formats/dtr/src/dtrplugin.cxx: In function 'void DDmkdir(const std::string&, mode_t, int, int)': mdtraj/formats/dtr/src/dtrplugin.cxx:714:30: warning: '%03x' directive writing between 3 and 8 bytes into a region of size 6 [-Wformat-overflow=] 714 | sprintf(subsub, "%03x", j); | ^~~~ mdtraj/formats/dtr/src/dtrplugin.cxx:714:29: note: directive argument in the range [0, 2147483646] 714 | sprintf(subsub, "%03x", j); | ^~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'void DDmkdir(const std::string&, mode_t, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:714:13: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 4 and 9 bytes into a destination of size 6 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ mdtraj/formats/dtr/src/dtrplugin.cxx: In function 'std::string framefile(const std::string&, size_t, size_t, int, int)': mdtraj/formats/dtr/src/dtrplugin.cxx:667:35: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=] 667 | sprintf(answer, "%03x/", d1); | ^ In function 'int sprintf(char*, const char*, ...)', inlined from 'std::string DDreldir(const std::string&, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:667:13, inlined from 'std::string framefile(const std::string&, size_t, size_t, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:771:23: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 5 and 10 bytes into a destination of size 9 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ mdtraj/formats/dtr/src/dtrplugin.cxx: In function 'std::string framefile(const std::string&, size_t, size_t, int, int)': mdtraj/formats/dtr/src/dtrplugin.cxx:665:35: warning: '%03x' directive writing between 3 and 8 bytes into a region of size between 0 and 5 [-Wformat-overflow=] 665 | sprintf(answer, "%03x/%03x/", d1, d2); | ^~~~ In function 'std::string DDreldir(const std::string&, int, int)', inlined from 'std::string framefile(const std::string&, size_t, size_t, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:771:23: mdtraj/formats/dtr/src/dtrplugin.cxx:665:29: note: directive argument in the range [0, 2147483646] 665 | sprintf(answer, "%03x/%03x/", d1, d2); | ^~~~~~~~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'std::string DDreldir(const std::string&, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:665:13, inlined from 'std::string framefile(const std::string&, size_t, size_t, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:771:23: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 9 and 19 bytes into a destination of size 9 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-311/mdtraj/formats/dtr/dtr.o build/temp.linux-aarch64-cpython-311/mdtraj/formats/dtr/src/dtrplugin.o -L/usr/lib/aarch64-linux-gnu -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/dtr.cpython-311-aarch64-linux-gnu.so building 'mdtraj._rmsd' extension aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/rmsd/_rmsd.cpp -o build/temp.linux-aarch64-cpython-311/mdtraj/rmsd/_rmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-aarch64-cpython-311/mdtraj/rmsd/src/center.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/rmsd/src/rotation.cpp -o build/temp.linux-aarch64-cpython-311/mdtraj/rmsd/src/rotation.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-aarch64-cpython-311/mdtraj/rmsd/src/theobald_rmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-311/mdtraj/rmsd/_rmsd.o build/temp.linux-aarch64-cpython-311/mdtraj/rmsd/src/center.o build/temp.linux-aarch64-cpython-311/mdtraj/rmsd/src/rotation.o build/temp.linux-aarch64-cpython-311/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/_rmsd.cpython-311-aarch64-linux-gnu.so building 'mdtraj._lprmsd' extension aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/rmsd/_lprmsd.cpp -o build/temp.linux-aarch64-cpython-311/mdtraj/rmsd/_lprmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1940, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/rmsd/_lprmsd.cpp:812: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/rmsd/src/Munkres.cpp -o build/temp.linux-aarch64-cpython-311/mdtraj/rmsd/src/Munkres.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-aarch64-cpython-311/mdtraj/rmsd/src/center.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/rmsd/src/euclidean_permutation.cpp -o build/temp.linux-aarch64-cpython-311/mdtraj/rmsd/src/euclidean_permutation.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/rmsd/src/fancy_index.cpp -o build/temp.linux-aarch64-cpython-311/mdtraj/rmsd/src/fancy_index.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/rmsd/src/rotation.cpp -o build/temp.linux-aarch64-cpython-311/mdtraj/rmsd/src/rotation.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-aarch64-cpython-311/mdtraj/rmsd/src/theobald_rmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-311/mdtraj/rmsd/_lprmsd.o build/temp.linux-aarch64-cpython-311/mdtraj/rmsd/src/Munkres.o build/temp.linux-aarch64-cpython-311/mdtraj/rmsd/src/center.o build/temp.linux-aarch64-cpython-311/mdtraj/rmsd/src/euclidean_permutation.o build/temp.linux-aarch64-cpython-311/mdtraj/rmsd/src/fancy_index.o build/temp.linux-aarch64-cpython-311/mdtraj/rmsd/src/rotation.o build/temp.linux-aarch64-cpython-311/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/_lprmsd.cpython-311-aarch64-linux-gnu.so building 'mdtraj.geometry._geometry' extension aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/geometry/src/_geometry.cpp -o build/temp.linux-aarch64-cpython-311/mdtraj/geometry/src/_geometry.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1940, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/geometry/src/_geometry.cpp:814: /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:6129:277: warning: '__pyx_v_offset[1]' may be used uninitialized [-Wmaybe-uninitialized] 6129 | (__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:6035:9: note: '__pyx_v_offset[1]' was declared here 6035 | float __pyx_v_offset[3]; | ^~~~~~~~~~~~~~ mdtraj/geometry/src/_geometry.cpp:6129:277: warning: '__pyx_v_delta[1]' may be used uninitialized [-Wmaybe-uninitialized] 6129 | (__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:6036:9: note: '__pyx_v_delta[1]' was declared here 6036 | float __pyx_v_delta[3]; | ^~~~~~~~~~~~~ mdtraj/geometry/src/_geometry.cpp:6115:224: warning: '__pyx_v_delta[2]' may be used uninitialized [-Wmaybe-uninitialized] 6115 | (__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:6036:9: note: '__pyx_v_delta[2]' was declared here 6036 | float __pyx_v_delta[3]; | ^~~~~~~~~~~~~ aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/geometry/src/dssp.cpp -o build/temp.linux-aarch64-cpython-311/mdtraj/geometry/src/dssp.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/geometry/src/geometry.cpp -o build/temp.linux-aarch64-cpython-311/mdtraj/geometry/src/geometry.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/geometry/src/sasa.cpp -o build/temp.linux-aarch64-cpython-311/mdtraj/geometry/src/sasa.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-311/mdtraj/geometry/src/_geometry.o build/temp.linux-aarch64-cpython-311/mdtraj/geometry/src/dssp.o build/temp.linux-aarch64-cpython-311/mdtraj/geometry/src/geometry.o build/temp.linux-aarch64-cpython-311/mdtraj/geometry/src/sasa.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/_geometry.cpython-311-aarch64-linux-gnu.so building 'mdtraj.geometry.drid' extension aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/geometry/drid.cpp -o build/temp.linux-aarch64-cpython-311/mdtraj/geometry/drid.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/geometry/src/dridkernels.cpp -o build/temp.linux-aarch64-cpython-311/mdtraj/geometry/src/dridkernels.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/geometry/src/moments.cpp -o build/temp.linux-aarch64-cpython-311/mdtraj/geometry/src/moments.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-311/mdtraj/geometry/drid.o build/temp.linux-aarch64-cpython-311/mdtraj/geometry/src/dridkernels.o build/temp.linux-aarch64-cpython-311/mdtraj/geometry/src/moments.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/drid.cpython-311-aarch64-linux-gnu.so building 'mdtraj.geometry.neighbors' extension aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/geometry/neighbors.cpp -o build/temp.linux-aarch64-cpython-311/mdtraj/geometry/neighbors.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/geometry/src/neighbors.cpp -o build/temp.linux-aarch64-cpython-311/mdtraj/geometry/src/neighbors.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-311/mdtraj/geometry/neighbors.o build/temp.linux-aarch64-cpython-311/mdtraj/geometry/src/neighbors.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/neighbors.cpython-311-aarch64-linux-gnu.so building 'mdtraj.geometry.neighborlist' extension aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/geometry/neighborlist.cpp -o build/temp.linux-aarch64-cpython-311/mdtraj/geometry/neighborlist.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/geometry/src/neighborlist.cpp -o build/temp.linux-aarch64-cpython-311/mdtraj/geometry/src/neighborlist.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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:51:53: warning: 'periodicBoxVectors' may be used uninitialized [-Wmaybe-uninitialized] 51 | periodicBoxSize[1] = periodicBoxVectors[1][1]; | ~~~~~~~~~~~~~~~~~~~~~~~^ 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:52:53: warning: 'periodicBoxVectors' may be used uninitialized [-Wmaybe-uninitialized] 52 | periodicBoxSize[2] = periodicBoxVectors[2][2]; | ~~~~~~~~~~~~~~~~~~~~~~~^ 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]; | ^~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-311/mdtraj/geometry/neighborlist.o build/temp.linux-aarch64-cpython-311/mdtraj/geometry/src/neighborlist.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/neighborlist.cpython-311-aarch64-linux-gnu.so dh_auto_test -O--buildsystem=pybuild pybuild --test -i python{version} -p "3.12 3.11" I: pybuild base:311: cd /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build; python3.12 -m unittest discover -v /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/netcdf.py:217: SyntaxWarning: invalid escape sequence '\g' """Read data from a molecular dynamics trajectory in the AMBER NetCDF /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/netcdf.py:323: SyntaxWarning: invalid escape sequence '\g' """Write one or more frames of a molecular dynamics trajectory to disk /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/amberrst.py:271: SyntaxWarning: invalid escape sequence '\g' """Read data from an AMBER ASCII restart file /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/amberrst.py:534: SyntaxWarning: invalid escape sequence '\g' """Read data from an AMBER NetCDF restart file /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/lammpstrj.py:237: SyntaxWarning: invalid escape sequence '\g' """Read data from a lammpstrj file. /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/lammpstrj.py:429: SyntaxWarning: invalid escape sequence '\g' """Write the box lines in the header of a frame. /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/lammpstrj.py:476: SyntaxWarning: invalid escape sequence '\g' """Write one or more frames of data to a lammpstrj file. /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/gro.py:394: SyntaxWarning: invalid escape sequence '\d' time = float(findall('t= *(\d+\.\d+)',comment)[-1]) /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/gro.py:500: SyntaxWarning: invalid escape sequence '\.' return match('^[-+]?[0-9]*\.?[0-9]*([eEdD][-+]?[0-9]+)?$',word) /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/prmtop.py:63: SyntaxWarning: invalid escape sequence '\.' FORMAT_RE_PATTERN = re.compile("([0-9]+)([a-zA-Z]+)([0-9]+)\.?([0-9]*)") /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/mol2.py:215: SyntaxWarning: invalid escape sequence '\s' index_col=0, header=None, sep="\s+", engine='python') /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/mol2.py:222: SyntaxWarning: invalid escape sequence '\s' atoms_frame = pd.read_csv(csv, sep="\s+", engine='python', header=None) /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/hbond.py:251: SyntaxWarning: invalid escape sequence '\c' """Compute the Kabsch-Sander hydrogen bond energy between each pair /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/contact.py:44: SyntaxWarning: invalid escape sequence '\s' """Compute the distance between pairs of residues in a trajectory. /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/shape.py:80: SyntaxWarning: invalid escape sequence '\l' """Compute the asphericity of a trajectory. /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/shape.py:105: SyntaxWarning: invalid escape sequence '\l' """Compute the acylindricity of a trajectory. /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/shape.py:130: SyntaxWarning: invalid escape sequence '\k' """Compute the relative shape anisotropy of a trajectory. /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/gsd.py:228: SyntaxWarning: invalid escape sequence '\g' """Write one or more frames of data to a gsd file. /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/nmr/shift_wrappers.py:214: SyntaxWarning: invalid escape sequence '\s' d = pd.read_table("./bb_details.dat", index_col=False, header=None, sep="\s+").drop([3], axis=1) /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/nmr/shift_wrappers.py:292: SyntaxWarning: invalid escape sequence '\s' d = pd.read_table("./trj%d_pred.tab" % i, names=names, header=None, sep="\s+", skiprows=lines_to_skip) /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing/docstrings.py:126: SyntaxWarning: invalid escape sequence '\d' m = re.search('takes at most (\d+) positional arguments', str(e)) /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing/docscrape.py:305: SyntaxWarning: invalid escape sequence '\w' if re.compile('^([\w., ]+=)?\s*[\w\.]+\(.*\)$').match(summary_str): /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing/docscrape.py:345: SyntaxWarning: invalid escape sequence '\*' return [self['Signature'].replace('*','\*')] + [''] /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing/docscrape.py:464: SyntaxWarning: invalid escape sequence '\*' argspec = argspec.replace('*','\*') /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing/docscrape.py:482: SyntaxWarning: invalid escape sequence '\*' signature = self['Signature'].replace('*', '\*') ---------------------------------------------------------------------- Ran 0 tests in 0.000s NO TESTS RAN I: pybuild base:311: cd /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build; python3.11 -m unittest discover -v ---------------------------------------------------------------------- Ran 0 tests in 0.000s OK rm -fr -- /tmp/dh-xdg-rundir-nsMD4PDd create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild rm -f -- debian/python3-mdtraj.substvars debian/python-mdtraj-doc.substvars rm -fr -- debian/.debhelper/generated/python3-mdtraj/ debian/python3-mdtraj/ debian/tmp/ debian/.debhelper/generated/python-mdtraj-doc/ debian/python-mdtraj-doc/ dh_installdirs -O--buildsystem=pybuild install -m0755 -d debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples/data dh_auto_install -O--buildsystem=pybuild install -m0755 -d /build/reproducible-path/mdtraj-1.9.9/debian/tmp pybuild --install -i python{version} -p "3.12 3.11" --dest-dir /build/reproducible-path/mdtraj-1.9.9/debian/tmp I: pybuild base:311: /usr/bin/python3.12 setup.py install --root /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj Using built-in specs. COLLECT_GCC=/usr/bin/aarch64-linux-gnu-gcc COLLECT_LTO_WRAPPER=/usr/libexec/gcc/aarch64-linux-gnu/13/lto-wrapper OFFLOAD_TARGET_NAMES=nvptx-none OFFLOAD_TARGET_DEFAULT=1 Target: aarch64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 13.2.0-23' --with-bugurl=file:///usr/share/doc/gcc-13/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-13 --program-prefix=aarch64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libquadmath --disable-libquadmath-support --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --enable-fix-cortex-a53-843419 --disable-werror --enable-offload-targets=nvptx-none=/build/reproducible-path/gcc-13-13.2.0/debian/tmp-nvptx/usr --enable-offload-defaulted --without-cuda-driver --enable-checking=release --build=aarch64-linux-gnu --host=aarch64-linux-gnu --target=aarch64-linux-gnu Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 13.2.0 (Debian 13.2.0-23) 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 SSE2 support... Did not detect SSE2 support Attempting to autodetect SSE3 support... Did not detect SSE3 support Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support Attempting to autodetect NEON support... Compiler supports NEON [ 1/12] Cythonizing mdtraj/formats/dcd/dcd.pyx [ 2/12] Cythonizing mdtraj/geometry/drid.pyx [ 3/12] Cythonizing mdtraj/geometry/neighborlist.pyx [ 4/12] Cythonizing mdtraj/geometry/neighbors.pyx [ 5/12] Cythonizing mdtraj/geometry/src/_geometry.pyx [ 6/12] Cythonizing mdtraj/rmsd/_lprmsd.pyx [ 7/12] Cythonizing mdtraj/formats/binpos/binpos.pyx [ 8/12] Cythonizing mdtraj/formats/dtr/dtr.pyx [ 9/12] Cythonizing mdtraj/formats/tng/tng.pyx [10/12] Cythonizing mdtraj/formats/xtc/trr.pyx [11/12] Cythonizing mdtraj/formats/xtc/xtc.pyx [12/12] Cythonizing mdtraj/rmsd/_rmsd.pyx running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running build running build_py copying mdtraj/version.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj running build_ext building 'mdtraj.formats.xtc' extension aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/src/xdrfile.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_decompress_coord_float': mdtraj/formats/xtc/src/xdrfile.c:788:32: warning: variable 'larger' set but not used [-Wunused-but-set-variable] 788 | int smallnum, smaller, larger, i, is_smaller, run; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c:785:23: warning: variable 'minidx' set but not used [-Wunused-but-set-variable] 785 | int smallidx, minidx, maxidx; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_compress_coord_float': mdtraj/formats/xtc/src/xdrfile.c:1016:13: warning: variable 'errval' set but not used [-Wunused-but-set-variable] 1016 | int errval=1; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_decompress_coord_double': mdtraj/formats/xtc/src/xdrfile.c:1305:32: warning: variable 'larger' set but not used [-Wunused-but-set-variable] 1305 | int smallnum, smaller, larger, i, is_smaller, run; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c:1302:23: warning: variable 'minidx' set but not used [-Wunused-but-set-variable] 1302 | int smallidx, minidx, maxidx; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_compress_coord_double': mdtraj/formats/xtc/src/xdrfile.c:1509:13: warning: variable 'errval' set but not used [-Wunused-but-set-variable] 1509 | int errval=1; | ^~~~~~ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/xtc/src/xdrfile_xtc.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/src/xdrfile_xtc.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/formats/xtc/src/xdrfile_xtc.c: In function 'xtc_coord': mdtraj/formats/xtc/src/xdrfile_xtc.c:66:15: warning: unused variable 'j' [-Wunused-variable] 66 | int i,j,result; | ^ mdtraj/formats/xtc/src/xdrfile_xtc.c:66:13: warning: unused variable 'i' [-Wunused-variable] 66 | int i,j,result; | ^ mdtraj/formats/xtc/src/xdrfile_xtc.c: In function 'read_xtc_nframes': mdtraj/formats/xtc/src/xdrfile_xtc.c:119:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 119 | if (NULL == xd) | ^~ mdtraj/formats/xtc/src/xdrfile_xtc.c:122:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 122 | do { | ^~ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/xtc/xtc.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/xtc.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1940, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/formats/xtc/xtc.c:784: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ In function '__Pyx_PyInt_From_int', inlined from '__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_16_write' at mdtraj/formats/xtc/xtc.c:9850:16: mdtraj/formats/xtc/xtc.c:696:40: warning: '__pyx_v_status' may be used uninitialized [-Wmaybe-uninitialized] 696 | #define PyInt_FromLong PyLong_FromLong | ^ mdtraj/formats/xtc/xtc.c:19348:20: note: in expansion of macro 'PyInt_FromLong' 19348 | return PyInt_FromLong((long) value); | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c: In function '__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_16_write': mdtraj/formats/xtc/xtc.c:9570:7: note: '__pyx_v_status' was declared here 9570 | int __pyx_v_status; | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c: In function '__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_12_read': mdtraj/formats/xtc/xtc.c:7672:17: warning: '__pyx_pybuffernd_framebuffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 7672 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_framebuffer.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6476:21: note: '__pyx_pybuffernd_framebuffer.diminfo[0].shape' was declared here 6476 | __Pyx_LocalBuf_ND __pyx_pybuffernd_framebuffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:7676:17: warning: '__pyx_pybuffernd_framebuffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 7676 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_framebuffer.diminfo[1].shape)) __pyx_t_6 = 1; | ^ mdtraj/formats/xtc/xtc.c:6476:21: note: '__pyx_pybuffernd_framebuffer.diminfo[1].shape' was declared here 6476 | __Pyx_LocalBuf_ND __pyx_pybuffernd_framebuffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8053:23: warning: '__pyx_pybuffernd_box_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8053 | } else if (unlikely(__pyx_t_32 >= __pyx_pybuffernd_box_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6474:21: note: '__pyx_pybuffernd_box_stride.diminfo[0].shape' was declared here 6474 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8057:23: warning: '__pyx_pybuffernd_box_stride.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8057 | } else if (unlikely(__pyx_t_33 >= __pyx_pybuffernd_box_stride.diminfo[1].shape)) __pyx_t_6 = 1; | ^ mdtraj/formats/xtc/xtc.c:6474:21: note: '__pyx_pybuffernd_box_stride.diminfo[1].shape' was declared here 6474 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8061:23: warning: '__pyx_pybuffernd_box_stride.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 8061 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_box_stride.diminfo[2].shape)) __pyx_t_6 = 2; | ^ mdtraj/formats/xtc/xtc.c:6474:21: note: '__pyx_pybuffernd_box_stride.diminfo[2].shape' was declared here 6474 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8099:23: warning: '__pyx_pybuffernd_prec_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8099 | } else if (unlikely(__pyx_t_40 >= __pyx_pybuffernd_prec_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6480:21: note: '__pyx_pybuffernd_prec_stride.diminfo[0].shape' was declared here 6480 | __Pyx_LocalBuf_ND __pyx_pybuffernd_prec_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8023:23: warning: '__pyx_pybuffernd_step_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8023 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_step_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6484:21: note: '__pyx_pybuffernd_step_stride.diminfo[0].shape' was declared here 6484 | __Pyx_LocalBuf_ND __pyx_pybuffernd_step_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8041:23: warning: '__pyx_pybuffernd_time_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8041 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_time_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6488:21: note: '__pyx_pybuffernd_time_stride.diminfo[0].shape' was declared here 6488 | __Pyx_LocalBuf_ND __pyx_pybuffernd_time_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8081:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8081 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_xyz_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6492:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[0].shape' was declared here 6492 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8085:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8085 | } else if (unlikely(__pyx_t_38 >= __pyx_pybuffernd_xyz_stride.diminfo[1].shape)) __pyx_t_6 = 1; | ^ mdtraj/formats/xtc/xtc.c:6492:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[1].shape' was declared here 6492 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8089:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 8089 | } else if (unlikely(__pyx_t_39 >= __pyx_pybuffernd_xyz_stride.diminfo[2].shape)) __pyx_t_6 = 2; | ^ mdtraj/formats/xtc/xtc.c:6492:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[2].shape' was declared here 6492 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/src/xdrfile_xtc.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/xtc.o -L/usr/lib/aarch64-linux-gnu -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/xtc.cpython-312-aarch64-linux-gnu.so building 'mdtraj.formats.trr' extension aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/src/xdrfile.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_decompress_coord_float': mdtraj/formats/xtc/src/xdrfile.c:788:32: warning: variable 'larger' set but not used [-Wunused-but-set-variable] 788 | int smallnum, smaller, larger, i, is_smaller, run; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c:785:23: warning: variable 'minidx' set but not used [-Wunused-but-set-variable] 785 | int smallidx, minidx, maxidx; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_compress_coord_float': mdtraj/formats/xtc/src/xdrfile.c:1016:13: warning: variable 'errval' set but not used [-Wunused-but-set-variable] 1016 | int errval=1; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_decompress_coord_double': mdtraj/formats/xtc/src/xdrfile.c:1305:32: warning: variable 'larger' set but not used [-Wunused-but-set-variable] 1305 | int smallnum, smaller, larger, i, is_smaller, run; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c:1302:23: warning: variable 'minidx' set but not used [-Wunused-but-set-variable] 1302 | int smallidx, minidx, maxidx; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_compress_coord_double': mdtraj/formats/xtc/src/xdrfile.c:1509:13: warning: variable 'errval' set but not used [-Wunused-but-set-variable] 1509 | int errval=1; | ^~~~~~ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/xtc/src/xdrfile_trr.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/src/xdrfile_trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/xtc/trr.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1940, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/formats/xtc/trr.c:784: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ In function '__Pyx_PyInt_From_int', inlined from '__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_18_write' at mdtraj/formats/xtc/trr.c:11623:16: mdtraj/formats/xtc/trr.c:696:40: warning: '__pyx_v_status' may be used uninitialized [-Wmaybe-uninitialized] 696 | #define PyInt_FromLong PyLong_FromLong | ^ mdtraj/formats/xtc/trr.c:21046:20: note: in expansion of macro 'PyInt_FromLong' 21046 | return PyInt_FromLong((long) value); | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c: In function '__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_18_write': mdtraj/formats/xtc/trr.c:11096:7: note: '__pyx_v_status' was declared here 11096 | int __pyx_v_status; | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c: In function '__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_14_read': mdtraj/formats/xtc/trr.c:8671:19: warning: '__pyx_pybuffernd_forces_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8671 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_forces_buffer.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/trr.c:6988:21: note: '__pyx_pybuffernd_forces_buffer.diminfo[0].shape' was declared here 6988 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8675:19: warning: '__pyx_pybuffernd_forces_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8675 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_forces_buffer.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:6988:21: note: '__pyx_pybuffernd_forces_buffer.diminfo[1].shape' was declared here 6988 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8619:19: warning: '__pyx_pybuffernd_vel_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8619 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_vel_buffer.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/trr.c:7004:21: note: '__pyx_pybuffernd_vel_buffer.diminfo[0].shape' was declared here 7004 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8623:19: warning: '__pyx_pybuffernd_vel_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8623 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_vel_buffer.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:7004:21: note: '__pyx_pybuffernd_vel_buffer.diminfo[1].shape' was declared here 7004 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8778:17: warning: '__pyx_pybuffernd_xyz_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8778 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_xyz_buffer.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/trr.c:7008:21: note: '__pyx_pybuffernd_xyz_buffer.diminfo[0].shape' was declared here 7008 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8782:17: warning: '__pyx_pybuffernd_xyz_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8782 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_xyz_buffer.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:7008:21: note: '__pyx_pybuffernd_xyz_buffer.diminfo[1].shape' was declared here 7008 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8384:19: warning: '__pyx_pybuffernd_vel.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8384 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_vel.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/trr.c:7002:21: note: '__pyx_pybuffernd_vel.diminfo[0].shape' was declared here 7002 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:1935:90: warning: '__pyx_pybuffernd_vel.diminfo[0].strides' may be used uninitialized [-Wmaybe-uninitialized] 1935 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) | ^ mdtraj/formats/xtc/trr.c:8397:42: note: in expansion of macro '__Pyx_BufPtrCContig3d' 8397 | __pyx_v_frame_vel = ((rvec *)(&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_vel.rcbuffer->pybuffer.buf, __pyx_t_29, __pyx_pybuffernd_vel.diminfo[0].strides, __pyx_t_30, __pyx_pybuffernd_vel.diminfo[1].strides, __pyx_t_31, __pyx_pybuffernd_vel.diminfo[2].strides)))); | ^~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:7002:21: note: '__pyx_pybuffernd_vel.diminfo[0].strides' was declared here 7002 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8388:19: warning: '__pyx_pybuffernd_vel.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8388 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_vel.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:7002:21: note: '__pyx_pybuffernd_vel.diminfo[1].shape' was declared here 7002 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8392:19: warning: '__pyx_pybuffernd_vel.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 8392 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_vel.diminfo[2].shape)) __pyx_t_5 = 2; | ^ mdtraj/formats/xtc/trr.c:7002:21: note: '__pyx_pybuffernd_vel.diminfo[2].shape' was declared here 7002 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8441:19: warning: '__pyx_pybuffernd_forces.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8441 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_forces.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/trr.c:6986:21: note: '__pyx_pybuffernd_forces.diminfo[0].shape' was declared here 6986 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:1935:90: warning: '__pyx_pybuffernd_forces.diminfo[0].strides' may be used uninitialized [-Wmaybe-uninitialized] 1935 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) | ^ mdtraj/formats/xtc/trr.c:8454:45: note: in expansion of macro '__Pyx_BufPtrCContig3d' 8454 | __pyx_v_frame_forces = ((rvec *)(&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_forces.rcbuffer->pybuffer.buf, __pyx_t_29, __pyx_pybuffernd_forces.diminfo[0].strides, __pyx_t_31, __pyx_pybuffernd_forces.diminfo[1].strides, __pyx_t_30, __pyx_pybuffernd_forces.diminfo[2].strides)))); | ^~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:6986:21: note: '__pyx_pybuffernd_forces.diminfo[0].strides' was declared here 6986 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8445:19: warning: '__pyx_pybuffernd_forces.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8445 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_forces.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:6986:21: note: '__pyx_pybuffernd_forces.diminfo[1].shape' was declared here 6986 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8449:19: warning: '__pyx_pybuffernd_forces.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 8449 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_forces.diminfo[2].shape)) __pyx_t_5 = 2; | ^ mdtraj/formats/xtc/trr.c:6986:21: note: '__pyx_pybuffernd_forces.diminfo[2].shape' was declared here 6986 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/src/xdrfile_trr.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/trr.o -L/usr/lib/aarch64-linux-gnu -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/trr.cpython-312-aarch64-linux-gnu.so building 'mdtraj.formats.tng' extension aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/tng/src/compression/bwlzh.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/bwlzh.o aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/tng/src/compression/bwt.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/bwt.o aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/tng/src/compression/coder.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/coder.o aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/tng/src/compression/dict.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/dict.o aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/tng/src/compression/fixpoint.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/fixpoint.o aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/tng/src/compression/huffman.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/huffman.o aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/tng/src/compression/huffmem.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/huffmem.o aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/tng/src/compression/lz77.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/lz77.o aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/tng/src/compression/merge_sort.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/merge_sort.o aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/tng/src/compression/mtf.c -o build/temp.linux-aarch64-cpython-312/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) | ^~ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/tng/src/compression/rle.c -o build/temp.linux-aarch64-cpython-312/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]) | ^~ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/tng/src/compression/tng_compress.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/tng_compress.o aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/tng/src/compression/vals16.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/vals16.o aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/tng/src/compression/warnmalloc.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/warnmalloc.o aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/tng/src/compression/widemuldiv.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/widemuldiv.o aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/tng/src/compression/xtc2.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/xtc2.o aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/tng/src/compression/xtc3.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/xtc3.o aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/tng/src/lib/md5.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/lib/md5.o aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/tng/src/lib/tng_io.c -o build/temp.linux-aarch64-cpython-312/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 = | ^ mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_gen_data_block_add': mdtraj/formats/tng/src/lib/tng_io.c:12613:9: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-truncation] 12613 | strncpy(data->block_name, block_name, strlen(block_name) + 1); | ^ 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); | ^~~~~~~~~~~~~~~~~~ In function 'tng_file_output_numerical', inlined from 'tng_data_block_write.isra' at mdtraj/formats/tng/src/lib/tng_io.c:5969:12: mdtraj/formats/tng/src/lib/tng_io.c:759:22: warning: 'n_particles' may be used uninitialized [-Wmaybe-uninitialized] 759 | temp_i64 = *((int64_t *)src); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_data_block_write.isra': 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; | ^~~~~~~~~~~ In function 'tng_file_output_numerical', inlined from 'tng_data_block_write.isra' at mdtraj/formats/tng/src/lib/tng_io.c:5962:12: mdtraj/formats/tng/src/lib/tng_io.c:759:22: warning: 'num_first_particle' may be used uninitialized [-Wmaybe-uninitialized] 759 | temp_i64 = *((int64_t *)src); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_data_block_write.isra': mdtraj/formats/tng/src/lib/tng_io.c:5684:26: note: 'num_first_particle' was declared here 5684 | int64_t n_particles, num_first_particle, n_frames, stride_length; | ^~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/tng/tng.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/tng.o In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1940, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/formats/tng/tng.c:810: /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:3706:104: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3706 | __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:3761:88: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3761 | __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:3793:90: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3793 | __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:3825:95: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3825 | __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:3895:113: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3895 | __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:3939:77: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3939 | __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:4735:106: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 4735 | __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:4780:108: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 4780 | __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:4887:115: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 4887 | __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:4917:105: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 4917 | __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:5045:105: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 5045 | __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:5646:126: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 5646 | __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:6056:152: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 6056 | __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:6324:108: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 6324 | __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:6426:304: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 6426 | __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:8918:94: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 8918 | __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:8950:75: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 8950 | __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:8982:81: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 8982 | __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:9305:77: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 9305 | __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:9496:372: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 9496 | __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:9548:378: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 9548 | __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:9610:89: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 9610 | __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); | ^~ aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/bwlzh.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/bwt.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/coder.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/dict.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/fixpoint.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/huffman.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/huffmem.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/lz77.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/merge_sort.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/mtf.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/rle.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/tng_compress.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/vals16.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/warnmalloc.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/widemuldiv.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/xtc2.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/compression/xtc3.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/lib/md5.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/src/lib/tng_io.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/tng/tng.o -L/usr/lib -L/usr/lib/aarch64-linux-gnu -lz -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/tng.cpython-312-aarch64-linux-gnu.so building 'mdtraj.formats.dcd' extension aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/dcd/dcd.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/dcd/dcd.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1940, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/formats/dcd/dcd.c:782: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ In function '__Pyx_PyInt_From_int', inlined from '__pyx_pf_6mdtraj_7formats_3dcd_17DCDTrajectoryFile_20read' at mdtraj/formats/dcd/dcd.c:6646:17: mdtraj/formats/dcd/dcd.c:694:40: warning: '__pyx_v_i' may be used uninitialized [-Wmaybe-uninitialized] 694 | #define PyInt_FromLong PyLong_FromLong | ^ mdtraj/formats/dcd/dcd.c:13600:20: note: in expansion of macro 'PyInt_FromLong' 13600 | return PyInt_FromLong((long) value); | ^~~~~~~~~~~~~~ mdtraj/formats/dcd/dcd.c: In function '__pyx_pf_6mdtraj_7formats_3dcd_17DCDTrajectoryFile_20read': mdtraj/formats/dcd/dcd.c:5465:7: note: '__pyx_v_i' was declared here 5465 | int __pyx_v_i; | ^~~~~~~~~ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/dcd/src/dcdplugin.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/dcd/src/dcdplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/mdtraj/formats/dcd/dcd.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/dcd/src/dcdplugin.o -L/usr/lib/aarch64-linux-gnu -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/dcd.cpython-312-aarch64-linux-gnu.so building 'mdtraj.formats.binpos' extension aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/binpos/binpos.c -o build/temp.linux-aarch64-cpython-312/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:1940, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/formats/binpos/binpos.c:782: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ In function '__pyx_pf_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_8_read', inlined from '__pyx_pw_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_9_read' at mdtraj/formats/binpos/binpos.c:4994:13: mdtraj/formats/binpos/binpos.c:5526:6: warning: '__pyx_v_status' may be used uninitialized [-Wmaybe-uninitialized] 5526 | if (__pyx_t_2) { | ^ mdtraj/formats/binpos/binpos.c: In function '__pyx_pw_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_9_read': mdtraj/formats/binpos/binpos.c:5006:7: note: '__pyx_v_status' was declared here 5006 | int __pyx_v_status; | ^~~~~~~~~~~~~~ In function '__Pyx_PyInt_From_int', inlined from '__pyx_pf_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_8_read' at mdtraj/formats/binpos/binpos.c:5536:17, inlined from '__pyx_pw_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_9_read' at mdtraj/formats/binpos/binpos.c:4994:13: mdtraj/formats/binpos/binpos.c:694:40: warning: '__pyx_v_i' may be used uninitialized [-Wmaybe-uninitialized] 694 | #define PyInt_FromLong PyLong_FromLong | ^ mdtraj/formats/binpos/binpos.c:13100:20: note: in expansion of macro 'PyInt_FromLong' 13100 | return PyInt_FromLong((long) value); | ^~~~~~~~~~~~~~ mdtraj/formats/binpos/binpos.c: In function '__pyx_pw_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_9_read': mdtraj/formats/binpos/binpos.c:5003:7: note: '__pyx_v_i' was declared here 5003 | int __pyx_v_i; | ^~~~~~~~~ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12 -c mdtraj/formats/binpos/src/binposplugin.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/binpos/src/binposplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/formats/binpos/src/binposplugin.c: In function 'open_binpos_read': mdtraj/formats/binpos/src/binposplugin.c:59:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 59 | fread(magicchar,sizeof(char),4,fd); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/binpos/src/binposplugin.c:69:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 69 | fread(&igarb,sizeof(int),1,fd); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/mdtraj/formats/binpos/binpos.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/binpos/src/binposplugin.o -L/usr/lib/aarch64-linux-gnu -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/binpos.cpython-312-aarch64-linux-gnu.so building 'mdtraj.formats.dtr' extension aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/dtr/dtr.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/dtr/dtr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1940, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/formats/dtr/dtr.cpp:803: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/dtr/src/dtrplugin.cxx -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/dtr/src/dtrplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ mdtraj/formats/dtr/src/dtrplugin.cxx: In member function 'bool desres::molfile::Timekeys::init(const std::string&)': mdtraj/formats/dtr/src/dtrplugin.cxx:487:27: warning: format '%d' expects argument of type 'int', but argument 2 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] 487 | printf("size %d framesize %d\n\n", | ~^ | | | int | %ld 488 | keys[i].size(), m_framesize); | ~~~~~~~~~~~~~~ | | | uint64_t {aka long unsigned int} mdtraj/formats/dtr/src/dtrplugin.cxx:487:40: warning: format '%d' expects argument of type 'int', but argument 3 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] 487 | printf("size %d framesize %d\n\n", | ~^ | | | int | %ld 488 | keys[i].size(), m_framesize); | ~~~~~~~~~~~ | | | uint64_t {aka long unsigned int} mdtraj/formats/dtr/src/dtrplugin.cxx: In constructor '{anonymous}::DDException::DDException(const std::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 std::string&, mode_t, int, int)': mdtraj/formats/dtr/src/dtrplugin.cxx:706:23: warning: '%03x' directive writing between 3 and 8 bytes into a region of size 6 [-Wformat-overflow=] 706 | sprintf(sub, "%03x/", i); | ^~~~ mdtraj/formats/dtr/src/dtrplugin.cxx:706:22: note: directive argument in the range [0, 2147483646] 706 | sprintf(sub, "%03x/", i); | ^~~~~~~ In file included from /usr/include/stdio.h:906, from mdtraj/formats/dtr/include/molfile_plugin.h:35, from mdtraj/formats/dtr/include/dtrplugin.hxx:46, from mdtraj/formats/dtr/src/dtrplugin.cxx:42: In function 'int sprintf(char*, const char*, ...)', inlined from 'void DDmkdir(const std::string&, mode_t, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:706:9: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 5 and 10 bytes into a destination of size 6 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ mdtraj/formats/dtr/src/dtrplugin.cxx: In function 'void DDmkdir(const std::string&, mode_t, int, int)': mdtraj/formats/dtr/src/dtrplugin.cxx:714:30: warning: '%03x' directive writing between 3 and 8 bytes into a region of size 6 [-Wformat-overflow=] 714 | sprintf(subsub, "%03x", j); | ^~~~ mdtraj/formats/dtr/src/dtrplugin.cxx:714:29: note: directive argument in the range [0, 2147483646] 714 | sprintf(subsub, "%03x", j); | ^~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'void DDmkdir(const std::string&, mode_t, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:714:13: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 4 and 9 bytes into a destination of size 6 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ mdtraj/formats/dtr/src/dtrplugin.cxx: In function 'std::string framefile(const std::string&, size_t, size_t, int, int)': mdtraj/formats/dtr/src/dtrplugin.cxx:667:35: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=] 667 | sprintf(answer, "%03x/", d1); | ^ In function 'int sprintf(char*, const char*, ...)', inlined from 'std::string DDreldir(const std::string&, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:667:13, inlined from 'std::string framefile(const std::string&, size_t, size_t, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:771:23: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 5 and 10 bytes into a destination of size 9 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ mdtraj/formats/dtr/src/dtrplugin.cxx: In function 'std::string framefile(const std::string&, size_t, size_t, int, int)': mdtraj/formats/dtr/src/dtrplugin.cxx:665:35: warning: '%03x' directive writing between 3 and 8 bytes into a region of size between 0 and 5 [-Wformat-overflow=] 665 | sprintf(answer, "%03x/%03x/", d1, d2); | ^~~~ In function 'std::string DDreldir(const std::string&, int, int)', inlined from 'std::string framefile(const std::string&, size_t, size_t, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:771:23: mdtraj/formats/dtr/src/dtrplugin.cxx:665:29: note: directive argument in the range [0, 2147483646] 665 | sprintf(answer, "%03x/%03x/", d1, d2); | ^~~~~~~~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'std::string DDreldir(const std::string&, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:665:13, inlined from 'std::string framefile(const std::string&, size_t, size_t, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:771:23: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 9 and 19 bytes into a destination of size 9 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/mdtraj/formats/dtr/dtr.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/dtr/src/dtrplugin.o -L/usr/lib/aarch64-linux-gnu -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/dtr.cpython-312-aarch64-linux-gnu.so building 'mdtraj._rmsd' extension aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/_rmsd.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/_rmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/center.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/rotation.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/rotation.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/theobald_rmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/_rmsd.o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/center.o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/rotation.o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/_rmsd.cpython-312-aarch64-linux-gnu.so building 'mdtraj._lprmsd' extension aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/_lprmsd.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/_lprmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1940, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/rmsd/_lprmsd.cpp:812: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/Munkres.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/Munkres.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/center.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/euclidean_permutation.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/euclidean_permutation.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/fancy_index.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/fancy_index.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/rotation.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/rotation.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/theobald_rmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/_lprmsd.o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/Munkres.o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/center.o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/euclidean_permutation.o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/fancy_index.o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/rotation.o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/_lprmsd.cpython-312-aarch64-linux-gnu.so building 'mdtraj.geometry._geometry' extension aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/src/_geometry.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/_geometry.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1940, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/geometry/src/_geometry.cpp:814: /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:6129:277: warning: '__pyx_v_offset[1]' may be used uninitialized [-Wmaybe-uninitialized] 6129 | (__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:6035:9: note: '__pyx_v_offset[1]' was declared here 6035 | float __pyx_v_offset[3]; | ^~~~~~~~~~~~~~ mdtraj/geometry/src/_geometry.cpp:6129:277: warning: '__pyx_v_delta[1]' may be used uninitialized [-Wmaybe-uninitialized] 6129 | (__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:6036:9: note: '__pyx_v_delta[1]' was declared here 6036 | float __pyx_v_delta[3]; | ^~~~~~~~~~~~~ mdtraj/geometry/src/_geometry.cpp:6115:224: warning: '__pyx_v_delta[2]' may be used uninitialized [-Wmaybe-uninitialized] 6115 | (__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:6036:9: note: '__pyx_v_delta[2]' was declared here 6036 | float __pyx_v_delta[3]; | ^~~~~~~~~~~~~ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/src/dssp.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/dssp.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/src/geometry.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/geometry.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/src/sasa.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/sasa.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/_geometry.o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/dssp.o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/geometry.o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/sasa.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/_geometry.cpython-312-aarch64-linux-gnu.so building 'mdtraj.geometry.drid' extension aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/drid.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/drid.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/src/dridkernels.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/dridkernels.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/src/moments.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/moments.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/mdtraj/geometry/drid.o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/dridkernels.o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/moments.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/drid.cpython-312-aarch64-linux-gnu.so building 'mdtraj.geometry.neighbors' extension aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/neighbors.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/neighbors.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/src/neighbors.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/neighbors.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/mdtraj/geometry/neighbors.o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/neighbors.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/neighbors.cpython-312-aarch64-linux-gnu.so building 'mdtraj.geometry.neighborlist' extension aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/neighborlist.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/neighborlist.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/src/neighborlist.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/neighborlist.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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:51:53: warning: 'periodicBoxVectors' may be used uninitialized [-Wmaybe-uninitialized] 51 | periodicBoxSize[1] = periodicBoxVectors[1][1]; | ~~~~~~~~~~~~~~~~~~~~~~~^ 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:52:53: warning: 'periodicBoxVectors' may be used uninitialized [-Wmaybe-uninitialized] 52 | periodicBoxSize[2] = periodicBoxVectors[2][2]; | ~~~~~~~~~~~~~~~~~~~~~~~^ 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]; | ^~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/mdtraj/geometry/neighborlist.o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/neighborlist.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/neighborlist.cpython-312-aarch64-linux-gnu.so running install_lib creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12 creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/_lprmsd.cpython-312-aarch64-linux-gnu.so -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/_rmsd.cpython-312-aarch64-linux-gnu.so -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/version.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/__pycache__/version.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/__pycache__ creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/__pycache__/trajectory.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/__pycache__/selection.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/__pycache__/residue_names.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/__pycache__/topology.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/__pycache__/element.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/__pycache__ creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/lib copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/lib/center.h -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/lib copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/lib/theobald_rmsd.h -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/lib copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/lib/libtheobald.a -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/lib copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/__init__.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/element.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/residue_names.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/selection.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/topology.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/trajectory.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/dtr.cpython-312-aarch64-linux-gnu.so -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/binpos.cpython-312-aarch64-linux-gnu.so -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/dcd.cpython-312-aarch64-linux-gnu.so -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/tng.cpython-312-aarch64-linux-gnu.so -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/trr.cpython-312-aarch64-linux-gnu.so -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/xtc.cpython-312-aarch64-linux-gnu.so -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/gsd.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/hoomdxml.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/mol2.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/psf.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/prmtop.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/openmmxml.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/pdbx.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/xyzfile.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/gro.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/lammpstrj.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/amberrst.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/mdcrd.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/lh5.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/netcdf.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/hdf5.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/registry.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/arc.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb/__pycache__/pdbstructure.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb/__pycache__/pdbfile.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb/__pycache__ creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb/data copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb/data/pdbNames.xml -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb/data copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb/data/residues.xml -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb/data copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb/__init__.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb/pdbfile.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb/pdbstructure.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__init__.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/amberrst.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/arc.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/gro.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/gsd.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/hdf5.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/hoomdxml.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/lammpstrj.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/lh5.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/mdcrd.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/mol2.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/netcdf.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/openmmxml.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdbx.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/prmtop.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/psf.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/registry.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/xyzfile.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/neighborlist.cpython-312-aarch64-linux-gnu.so -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/neighbors.cpython-312-aarch64-linux-gnu.so -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/drid.cpython-312-aarch64-linux-gnu.so -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/_geometry.cpython-312-aarch64-linux-gnu.so -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/shape.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/order.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/rdf.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/thermodynamic_properties.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/dssp.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/contact.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/sasa.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/hbond.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/dihedral.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/distance.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/angle.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/rg.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__init__.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/alignment.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/angle.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/contact.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/dihedral.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/distance.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/dssp.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/hbond.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/internal.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/order.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/rdf.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/rg.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/sasa.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/shape.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/thermodynamic_properties.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/nmr creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/nmr/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/nmr/__pycache__/scalar_couplings.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/nmr/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/nmr/__pycache__/shift_wrappers.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/nmr/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/nmr/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/nmr/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/nmr/__init__.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/nmr copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/nmr/scalar_couplings.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/nmr copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/nmr/shift_wrappers.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/nmr creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/__pycache__/xtcreporter.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/__pycache__/dcdreporter.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/__pycache__/netcdfreporter.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/__pycache__/basereporter.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/__pycache__/hdf5reporter.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/__init__.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/basereporter.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/dcdreporter.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/hdf5reporter.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/netcdfreporter.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/xtcreporter.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/scripts creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/scripts/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/scripts/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/scripts/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/scripts/__init__.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/scripts copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/scripts/mdconvert.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/scripts copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/scripts/mdinspect.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/scripts creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing/__pycache__/docscrape.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing/__pycache__/docstrings.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing/__pycache__/testing.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing/__init__.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing/docscrape.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing/docstrings.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing/testing.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/__pycache__/singleton.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/__pycache__/zipped.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/__pycache__/contextmanagers.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/__pycache__/unitcell.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/__pycache__/rotation.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/__pycache__/six.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/__pycache__/validation.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/__pycache__/delay_import.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/__pycache__ creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/__pycache__/prefix.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/__pycache__/unit_operators.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/__pycache__/unit_definitions.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/__pycache__/baseunit.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/__pycache__/mymatrix.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/__pycache__/unit.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/__pycache__/basedimension.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/__pycache__/standard_dimensions.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/__pycache__/quantity.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/__init__.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/mymatrix.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/constants.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/prefix.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/quantity.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/standard_dimensions.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/unit_definitions.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/unit_math.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/unit_operators.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/basedimension.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/baseunit.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/doctests.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/unit.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/__init__.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/contextmanagers.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/delay_import.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/rotation.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/singleton.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/six.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unitcell.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/validation.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/zipped.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/__init__.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/io.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/version.py to version.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/element.py to element.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/residue_names.py to residue_names.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/selection.py to selection.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/topology.py to topology.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/trajectory.py to trajectory.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb/pdbfile.py to pdbfile.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb/pdbstructure.py to pdbstructure.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/amberrst.py to amberrst.cpython-312.pyc /usr/lib/python3.12/dist-packages/mdtraj/formats/amberrst.py:271: SyntaxWarning: invalid escape sequence '\g' /usr/lib/python3.12/dist-packages/mdtraj/formats/amberrst.py:534: SyntaxWarning: invalid escape sequence '\g' byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/arc.py to arc.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/gro.py to gro.cpython-312.pyc /usr/lib/python3.12/dist-packages/mdtraj/formats/gro.py:394: SyntaxWarning: invalid escape sequence '\d' /usr/lib/python3.12/dist-packages/mdtraj/formats/gro.py:500: SyntaxWarning: invalid escape sequence '\.' byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/gsd.py to gsd.cpython-312.pyc /usr/lib/python3.12/dist-packages/mdtraj/formats/gsd.py:228: SyntaxWarning: invalid escape sequence '\g' byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/hdf5.py to hdf5.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/hoomdxml.py to hoomdxml.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/lammpstrj.py to lammpstrj.cpython-312.pyc /usr/lib/python3.12/dist-packages/mdtraj/formats/lammpstrj.py:237: SyntaxWarning: invalid escape sequence '\g' /usr/lib/python3.12/dist-packages/mdtraj/formats/lammpstrj.py:429: SyntaxWarning: invalid escape sequence '\g' /usr/lib/python3.12/dist-packages/mdtraj/formats/lammpstrj.py:476: SyntaxWarning: invalid escape sequence '\g' byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/lh5.py to lh5.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/mdcrd.py to mdcrd.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/mol2.py to mol2.cpython-312.pyc /usr/lib/python3.12/dist-packages/mdtraj/formats/mol2.py:215: SyntaxWarning: invalid escape sequence '\s' /usr/lib/python3.12/dist-packages/mdtraj/formats/mol2.py:222: SyntaxWarning: invalid escape sequence '\s' byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/netcdf.py to netcdf.cpython-312.pyc /usr/lib/python3.12/dist-packages/mdtraj/formats/netcdf.py:217: SyntaxWarning: invalid escape sequence '\g' /usr/lib/python3.12/dist-packages/mdtraj/formats/netcdf.py:323: SyntaxWarning: invalid escape sequence '\g' byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/openmmxml.py to openmmxml.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdbx.py to pdbx.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/prmtop.py to prmtop.cpython-312.pyc /usr/lib/python3.12/dist-packages/mdtraj/formats/prmtop.py:63: SyntaxWarning: invalid escape sequence '\.' byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/psf.py to psf.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/registry.py to registry.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/xyzfile.py to xyzfile.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/alignment.py to alignment.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/angle.py to angle.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/contact.py to contact.cpython-312.pyc /usr/lib/python3.12/dist-packages/mdtraj/geometry/contact.py:44: SyntaxWarning: invalid escape sequence '\s' byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/dihedral.py to dihedral.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/distance.py to distance.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/dssp.py to dssp.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/hbond.py to hbond.cpython-312.pyc /usr/lib/python3.12/dist-packages/mdtraj/geometry/hbond.py:251: SyntaxWarning: invalid escape sequence '\c' byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/internal.py to internal.cpython-312.pyc /usr/lib/python3.12/dist-packages/mdtraj/geometry/internal.py:370: SyntaxWarning: invalid escape sequence '\p' byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/order.py to order.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/rdf.py to rdf.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/rg.py to rg.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/sasa.py to sasa.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/shape.py to shape.cpython-312.pyc /usr/lib/python3.12/dist-packages/mdtraj/geometry/shape.py:80: SyntaxWarning: invalid escape sequence '\l' /usr/lib/python3.12/dist-packages/mdtraj/geometry/shape.py:105: SyntaxWarning: invalid escape sequence '\l' /usr/lib/python3.12/dist-packages/mdtraj/geometry/shape.py:130: SyntaxWarning: invalid escape sequence '\k' byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/thermodynamic_properties.py to thermodynamic_properties.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/nmr/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/nmr/scalar_couplings.py to scalar_couplings.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/nmr/shift_wrappers.py to shift_wrappers.cpython-312.pyc /usr/lib/python3.12/dist-packages/mdtraj/nmr/shift_wrappers.py:214: SyntaxWarning: invalid escape sequence '\s' /usr/lib/python3.12/dist-packages/mdtraj/nmr/shift_wrappers.py:292: SyntaxWarning: invalid escape sequence '\s' byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/basereporter.py to basereporter.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/dcdreporter.py to dcdreporter.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/hdf5reporter.py to hdf5reporter.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/netcdfreporter.py to netcdfreporter.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/xtcreporter.py to xtcreporter.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/scripts/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/scripts/mdconvert.py to mdconvert.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/scripts/mdinspect.py to mdinspect.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing/docscrape.py to docscrape.cpython-312.pyc /usr/lib/python3.12/dist-packages/mdtraj/testing/docscrape.py:305: SyntaxWarning: invalid escape sequence '\w' /usr/lib/python3.12/dist-packages/mdtraj/testing/docscrape.py:345: SyntaxWarning: invalid escape sequence '\*' /usr/lib/python3.12/dist-packages/mdtraj/testing/docscrape.py:464: SyntaxWarning: invalid escape sequence '\*' /usr/lib/python3.12/dist-packages/mdtraj/testing/docscrape.py:482: SyntaxWarning: invalid escape sequence '\*' byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing/docstrings.py to docstrings.cpython-312.pyc /usr/lib/python3.12/dist-packages/mdtraj/testing/docstrings.py:126: SyntaxWarning: invalid escape sequence '\d' byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing/testing.py to testing.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/mymatrix.py to mymatrix.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/constants.py to constants.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/prefix.py to prefix.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/quantity.py to quantity.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/standard_dimensions.py to standard_dimensions.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/unit_definitions.py to unit_definitions.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/unit_math.py to unit_math.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/unit_operators.py to unit_operators.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/basedimension.py to basedimension.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/baseunit.py to baseunit.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/doctests.py to doctests.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/unit.py to unit.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/contextmanagers.py to contextmanagers.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/delay_import.py to delay_import.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/rotation.py to rotation.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/singleton.py to singleton.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/six.py to six.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unitcell.py to unitcell.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/validation.py to validation.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/zipped.py to zipped.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/io.py to io.cpython-312.pyc running install_egg_info running egg_info creating mdtraj.egg-info writing mdtraj.egg-info/PKG-INFO writing dependency_links to mdtraj.egg-info/dependency_links.txt writing entry points to mdtraj.egg-info/entry_points.txt writing requirements to mdtraj.egg-info/requires.txt writing top-level names to mdtraj.egg-info/top_level.txt writing manifest file 'mdtraj.egg-info/SOURCES.txt' dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative reading manifest file 'mdtraj.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' no previously-included directories found matching '__pycache__' no previously-included directories found matching '*.pyc' adding license file 'LICENSE' writing manifest file 'mdtraj.egg-info/SOURCES.txt' Copying mdtraj.egg-info to /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj-1.9.9.egg-info Skipping SOURCES.txt running install_scripts Installing mdconvert-mdtraj script to /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/bin Installing mdinspect script to /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/bin I: pybuild base:311: /usr/bin/python3 setup.py install --root /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj Using built-in specs. COLLECT_GCC=/usr/bin/aarch64-linux-gnu-gcc COLLECT_LTO_WRAPPER=/usr/libexec/gcc/aarch64-linux-gnu/13/lto-wrapper OFFLOAD_TARGET_NAMES=nvptx-none OFFLOAD_TARGET_DEFAULT=1 Target: aarch64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 13.2.0-23' --with-bugurl=file:///usr/share/doc/gcc-13/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-13 --program-prefix=aarch64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libquadmath --disable-libquadmath-support --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --enable-fix-cortex-a53-843419 --disable-werror --enable-offload-targets=nvptx-none=/build/reproducible-path/gcc-13-13.2.0/debian/tmp-nvptx/usr --enable-offload-defaulted --without-cuda-driver --enable-checking=release --build=aarch64-linux-gnu --host=aarch64-linux-gnu --target=aarch64-linux-gnu Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 13.2.0 (Debian 13.2.0-23) 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 SSE2 support... Did not detect SSE2 support Attempting to autodetect SSE3 support... Did not detect SSE3 support Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support Attempting to autodetect NEON support... Compiler supports NEON [ 1/12] Cythonizing mdtraj/formats/dcd/dcd.pyx [ 2/12] Cythonizing mdtraj/geometry/drid.pyx [ 3/12] Cythonizing mdtraj/geometry/neighborlist.pyx [ 4/12] Cythonizing mdtraj/geometry/neighbors.pyx [ 5/12] Cythonizing mdtraj/geometry/src/_geometry.pyx [ 6/12] Cythonizing mdtraj/rmsd/_lprmsd.pyx [ 7/12] Cythonizing mdtraj/formats/binpos/binpos.pyx [ 8/12] Cythonizing mdtraj/formats/dtr/dtr.pyx [ 9/12] Cythonizing mdtraj/formats/tng/tng.pyx [10/12] Cythonizing mdtraj/formats/xtc/trr.pyx [11/12] Cythonizing mdtraj/formats/xtc/xtc.pyx [12/12] Cythonizing mdtraj/rmsd/_rmsd.pyx running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running build running build_py copying mdtraj/version.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj running build_ext building 'mdtraj.formats.xtc' extension aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.linux-aarch64-cpython-311/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-aarch64-cpython-311/mdtraj/formats/xtc/src/xdrfile.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_decompress_coord_float': mdtraj/formats/xtc/src/xdrfile.c:788:32: warning: variable 'larger' set but not used [-Wunused-but-set-variable] 788 | int smallnum, smaller, larger, i, is_smaller, run; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c:785:23: warning: variable 'minidx' set but not used [-Wunused-but-set-variable] 785 | int smallidx, minidx, maxidx; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_compress_coord_float': mdtraj/formats/xtc/src/xdrfile.c:1016:13: warning: variable 'errval' set but not used [-Wunused-but-set-variable] 1016 | int errval=1; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_decompress_coord_double': mdtraj/formats/xtc/src/xdrfile.c:1305:32: warning: variable 'larger' set but not used [-Wunused-but-set-variable] 1305 | int smallnum, smaller, larger, i, is_smaller, run; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c:1302:23: warning: variable 'minidx' set but not used [-Wunused-but-set-variable] 1302 | int smallidx, minidx, maxidx; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_compress_coord_double': mdtraj/formats/xtc/src/xdrfile.c:1509:13: warning: variable 'errval' set but not used [-Wunused-but-set-variable] 1509 | int errval=1; | ^~~~~~ aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/xtc/src/xdrfile_xtc.c -o build/temp.linux-aarch64-cpython-311/mdtraj/formats/xtc/src/xdrfile_xtc.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/formats/xtc/src/xdrfile_xtc.c: In function 'xtc_coord': mdtraj/formats/xtc/src/xdrfile_xtc.c:66:15: warning: unused variable 'j' [-Wunused-variable] 66 | int i,j,result; | ^ mdtraj/formats/xtc/src/xdrfile_xtc.c:66:13: warning: unused variable 'i' [-Wunused-variable] 66 | int i,j,result; | ^ mdtraj/formats/xtc/src/xdrfile_xtc.c: In function 'read_xtc_nframes': mdtraj/formats/xtc/src/xdrfile_xtc.c:119:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 119 | if (NULL == xd) | ^~ mdtraj/formats/xtc/src/xdrfile_xtc.c:122:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 122 | do { | ^~ aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/xtc/xtc.c -o build/temp.linux-aarch64-cpython-311/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:1940, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/formats/xtc/xtc.c:784: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ In function '__Pyx_PyInt_From_int', inlined from '__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_16_write' at mdtraj/formats/xtc/xtc.c:9850:16: mdtraj/formats/xtc/xtc.c:696:40: warning: '__pyx_v_status' may be used uninitialized [-Wmaybe-uninitialized] 696 | #define PyInt_FromLong PyLong_FromLong | ^ mdtraj/formats/xtc/xtc.c:19348:20: note: in expansion of macro 'PyInt_FromLong' 19348 | return PyInt_FromLong((long) value); | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c: In function '__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_16_write': mdtraj/formats/xtc/xtc.c:9570:7: note: '__pyx_v_status' was declared here 9570 | int __pyx_v_status; | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c: In function '__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_12_read': mdtraj/formats/xtc/xtc.c:7672:17: warning: '__pyx_pybuffernd_framebuffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 7672 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_framebuffer.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6476:21: note: '__pyx_pybuffernd_framebuffer.diminfo[0].shape' was declared here 6476 | __Pyx_LocalBuf_ND __pyx_pybuffernd_framebuffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:7676:17: warning: '__pyx_pybuffernd_framebuffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 7676 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_framebuffer.diminfo[1].shape)) __pyx_t_6 = 1; | ^ mdtraj/formats/xtc/xtc.c:6476:21: note: '__pyx_pybuffernd_framebuffer.diminfo[1].shape' was declared here 6476 | __Pyx_LocalBuf_ND __pyx_pybuffernd_framebuffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8053:23: warning: '__pyx_pybuffernd_box_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8053 | } else if (unlikely(__pyx_t_32 >= __pyx_pybuffernd_box_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6474:21: note: '__pyx_pybuffernd_box_stride.diminfo[0].shape' was declared here 6474 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8057:23: warning: '__pyx_pybuffernd_box_stride.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8057 | } else if (unlikely(__pyx_t_33 >= __pyx_pybuffernd_box_stride.diminfo[1].shape)) __pyx_t_6 = 1; | ^ mdtraj/formats/xtc/xtc.c:6474:21: note: '__pyx_pybuffernd_box_stride.diminfo[1].shape' was declared here 6474 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8061:23: warning: '__pyx_pybuffernd_box_stride.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 8061 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_box_stride.diminfo[2].shape)) __pyx_t_6 = 2; | ^ mdtraj/formats/xtc/xtc.c:6474:21: note: '__pyx_pybuffernd_box_stride.diminfo[2].shape' was declared here 6474 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8099:23: warning: '__pyx_pybuffernd_prec_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8099 | } else if (unlikely(__pyx_t_40 >= __pyx_pybuffernd_prec_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6480:21: note: '__pyx_pybuffernd_prec_stride.diminfo[0].shape' was declared here 6480 | __Pyx_LocalBuf_ND __pyx_pybuffernd_prec_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8023:23: warning: '__pyx_pybuffernd_step_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8023 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_step_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6484:21: note: '__pyx_pybuffernd_step_stride.diminfo[0].shape' was declared here 6484 | __Pyx_LocalBuf_ND __pyx_pybuffernd_step_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8041:23: warning: '__pyx_pybuffernd_time_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8041 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_time_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6488:21: note: '__pyx_pybuffernd_time_stride.diminfo[0].shape' was declared here 6488 | __Pyx_LocalBuf_ND __pyx_pybuffernd_time_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8081:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8081 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_xyz_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6492:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[0].shape' was declared here 6492 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8085:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8085 | } else if (unlikely(__pyx_t_38 >= __pyx_pybuffernd_xyz_stride.diminfo[1].shape)) __pyx_t_6 = 1; | ^ mdtraj/formats/xtc/xtc.c:6492:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[1].shape' was declared here 6492 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8089:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 8089 | } else if (unlikely(__pyx_t_39 >= __pyx_pybuffernd_xyz_stride.diminfo[2].shape)) __pyx_t_6 = 2; | ^ mdtraj/formats/xtc/xtc.c:6492:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[2].shape' was declared here 6492 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-311/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-aarch64-cpython-311/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-aarch64-cpython-311/mdtraj/formats/xtc/src/xdrfile_xtc.o build/temp.linux-aarch64-cpython-311/mdtraj/formats/xtc/xtc.o -L/usr/lib/aarch64-linux-gnu -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/xtc.cpython-311-aarch64-linux-gnu.so building 'mdtraj.formats.trr' extension aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.linux-aarch64-cpython-311/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-aarch64-cpython-311/mdtraj/formats/xtc/src/xdrfile.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_decompress_coord_float': mdtraj/formats/xtc/src/xdrfile.c:788:32: warning: variable 'larger' set but not used [-Wunused-but-set-variable] 788 | int smallnum, smaller, larger, i, is_smaller, run; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c:785:23: warning: variable 'minidx' set but not used [-Wunused-but-set-variable] 785 | int smallidx, minidx, maxidx; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_compress_coord_float': mdtraj/formats/xtc/src/xdrfile.c:1016:13: warning: variable 'errval' set but not used [-Wunused-but-set-variable] 1016 | int errval=1; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_decompress_coord_double': mdtraj/formats/xtc/src/xdrfile.c:1305:32: warning: variable 'larger' set but not used [-Wunused-but-set-variable] 1305 | int smallnum, smaller, larger, i, is_smaller, run; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c:1302:23: warning: variable 'minidx' set but not used [-Wunused-but-set-variable] 1302 | int smallidx, minidx, maxidx; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_compress_coord_double': mdtraj/formats/xtc/src/xdrfile.c:1509:13: warning: variable 'errval' set but not used [-Wunused-but-set-variable] 1509 | int errval=1; | ^~~~~~ aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/xtc/src/xdrfile_trr.c -o build/temp.linux-aarch64-cpython-311/mdtraj/formats/xtc/src/xdrfile_trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/xtc/trr.c -o build/temp.linux-aarch64-cpython-311/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:1940, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/formats/xtc/trr.c:784: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ In function '__Pyx_PyInt_From_int', inlined from '__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_18_write' at mdtraj/formats/xtc/trr.c:11623:16: mdtraj/formats/xtc/trr.c:696:40: warning: '__pyx_v_status' may be used uninitialized [-Wmaybe-uninitialized] 696 | #define PyInt_FromLong PyLong_FromLong | ^ mdtraj/formats/xtc/trr.c:21046:20: note: in expansion of macro 'PyInt_FromLong' 21046 | return PyInt_FromLong((long) value); | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c: In function '__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_18_write': mdtraj/formats/xtc/trr.c:11096:7: note: '__pyx_v_status' was declared here 11096 | int __pyx_v_status; | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c: In function '__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_14_read': mdtraj/formats/xtc/trr.c:8671:19: warning: '__pyx_pybuffernd_forces_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8671 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_forces_buffer.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/trr.c:6988:21: note: '__pyx_pybuffernd_forces_buffer.diminfo[0].shape' was declared here 6988 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8675:19: warning: '__pyx_pybuffernd_forces_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8675 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_forces_buffer.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:6988:21: note: '__pyx_pybuffernd_forces_buffer.diminfo[1].shape' was declared here 6988 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8619:19: warning: '__pyx_pybuffernd_vel_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8619 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_vel_buffer.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/trr.c:7004:21: note: '__pyx_pybuffernd_vel_buffer.diminfo[0].shape' was declared here 7004 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8623:19: warning: '__pyx_pybuffernd_vel_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8623 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_vel_buffer.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:7004:21: note: '__pyx_pybuffernd_vel_buffer.diminfo[1].shape' was declared here 7004 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8778:17: warning: '__pyx_pybuffernd_xyz_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8778 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_xyz_buffer.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/trr.c:7008:21: note: '__pyx_pybuffernd_xyz_buffer.diminfo[0].shape' was declared here 7008 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8782:17: warning: '__pyx_pybuffernd_xyz_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8782 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_xyz_buffer.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:7008:21: note: '__pyx_pybuffernd_xyz_buffer.diminfo[1].shape' was declared here 7008 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8384:19: warning: '__pyx_pybuffernd_vel.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8384 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_vel.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/trr.c:7002:21: note: '__pyx_pybuffernd_vel.diminfo[0].shape' was declared here 7002 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:1935:90: warning: '__pyx_pybuffernd_vel.diminfo[0].strides' may be used uninitialized [-Wmaybe-uninitialized] 1935 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) | ^ mdtraj/formats/xtc/trr.c:8397:42: note: in expansion of macro '__Pyx_BufPtrCContig3d' 8397 | __pyx_v_frame_vel = ((rvec *)(&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_vel.rcbuffer->pybuffer.buf, __pyx_t_29, __pyx_pybuffernd_vel.diminfo[0].strides, __pyx_t_30, __pyx_pybuffernd_vel.diminfo[1].strides, __pyx_t_31, __pyx_pybuffernd_vel.diminfo[2].strides)))); | ^~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:7002:21: note: '__pyx_pybuffernd_vel.diminfo[0].strides' was declared here 7002 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8388:19: warning: '__pyx_pybuffernd_vel.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8388 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_vel.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:7002:21: note: '__pyx_pybuffernd_vel.diminfo[1].shape' was declared here 7002 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8392:19: warning: '__pyx_pybuffernd_vel.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 8392 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_vel.diminfo[2].shape)) __pyx_t_5 = 2; | ^ mdtraj/formats/xtc/trr.c:7002:21: note: '__pyx_pybuffernd_vel.diminfo[2].shape' was declared here 7002 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8441:19: warning: '__pyx_pybuffernd_forces.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8441 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_forces.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/trr.c:6986:21: note: '__pyx_pybuffernd_forces.diminfo[0].shape' was declared here 6986 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:1935:90: warning: '__pyx_pybuffernd_forces.diminfo[0].strides' may be used uninitialized [-Wmaybe-uninitialized] 1935 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) | ^ mdtraj/formats/xtc/trr.c:8454:45: note: in expansion of macro '__Pyx_BufPtrCContig3d' 8454 | __pyx_v_frame_forces = ((rvec *)(&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_forces.rcbuffer->pybuffer.buf, __pyx_t_29, __pyx_pybuffernd_forces.diminfo[0].strides, __pyx_t_31, __pyx_pybuffernd_forces.diminfo[1].strides, __pyx_t_30, __pyx_pybuffernd_forces.diminfo[2].strides)))); | ^~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:6986:21: note: '__pyx_pybuffernd_forces.diminfo[0].strides' was declared here 6986 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8445:19: warning: '__pyx_pybuffernd_forces.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8445 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_forces.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:6986:21: note: '__pyx_pybuffernd_forces.diminfo[1].shape' was declared here 6986 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8449:19: warning: '__pyx_pybuffernd_forces.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 8449 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_forces.diminfo[2].shape)) __pyx_t_5 = 2; | ^ mdtraj/formats/xtc/trr.c:6986:21: note: '__pyx_pybuffernd_forces.diminfo[2].shape' was declared here 6986 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-311/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-aarch64-cpython-311/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-aarch64-cpython-311/mdtraj/formats/xtc/src/xdrfile_trr.o build/temp.linux-aarch64-cpython-311/mdtraj/formats/xtc/trr.o -L/usr/lib/aarch64-linux-gnu -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/trr.cpython-311-aarch64-linux-gnu.so building 'mdtraj.formats.tng' extension aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/tng/src/compression/bwlzh.c -o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/bwlzh.o aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/tng/src/compression/bwt.c -o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/bwt.o aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/tng/src/compression/coder.c -o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/coder.o aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/tng/src/compression/dict.c -o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/dict.o aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/tng/src/compression/fixpoint.c -o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/fixpoint.o aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/tng/src/compression/huffman.c -o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/huffman.o aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/tng/src/compression/huffmem.c -o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/huffmem.o aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/tng/src/compression/lz77.c -o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/lz77.o aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/tng/src/compression/merge_sort.c -o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/merge_sort.o aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/tng/src/compression/mtf.c -o build/temp.linux-aarch64-cpython-311/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) | ^~ aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/tng/src/compression/rle.c -o build/temp.linux-aarch64-cpython-311/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]) | ^~ aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/tng/src/compression/tng_compress.c -o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/tng_compress.o aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/tng/src/compression/vals16.c -o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/vals16.o aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/tng/src/compression/warnmalloc.c -o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/warnmalloc.o aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/tng/src/compression/widemuldiv.c -o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/widemuldiv.o aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/tng/src/compression/xtc2.c -o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/xtc2.o aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/tng/src/compression/xtc3.c -o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/xtc3.o aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/tng/src/lib/md5.c -o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/lib/md5.o aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/tng/src/lib/tng_io.c -o build/temp.linux-aarch64-cpython-311/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 = | ^ mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_gen_data_block_add': mdtraj/formats/tng/src/lib/tng_io.c:12613:9: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-truncation] 12613 | strncpy(data->block_name, block_name, strlen(block_name) + 1); | ^ 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); | ^~~~~~~~~~~~~~~~~~ In function 'tng_file_output_numerical', inlined from 'tng_data_block_write.isra' at mdtraj/formats/tng/src/lib/tng_io.c:5969:12: mdtraj/formats/tng/src/lib/tng_io.c:759:22: warning: 'n_particles' may be used uninitialized [-Wmaybe-uninitialized] 759 | temp_i64 = *((int64_t *)src); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_data_block_write.isra': 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; | ^~~~~~~~~~~ In function 'tng_file_output_numerical', inlined from 'tng_data_block_write.isra' at mdtraj/formats/tng/src/lib/tng_io.c:5962:12: mdtraj/formats/tng/src/lib/tng_io.c:759:22: warning: 'num_first_particle' may be used uninitialized [-Wmaybe-uninitialized] 759 | temp_i64 = *((int64_t *)src); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_data_block_write.isra': mdtraj/formats/tng/src/lib/tng_io.c:5684:26: note: 'num_first_particle' was declared here 5684 | int64_t n_particles, num_first_particle, n_frames, stride_length; | ^~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/tng/tng.c -o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/tng.o In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1940, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/formats/tng/tng.c:810: /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:3706:104: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3706 | __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:3761:88: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3761 | __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:3793:90: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3793 | __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:3825:95: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3825 | __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:3895:113: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3895 | __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:3939:77: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3939 | __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:4735:106: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 4735 | __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:4780:108: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 4780 | __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:4887:115: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 4887 | __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:4917:105: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 4917 | __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:5045:105: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 5045 | __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:5646:126: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 5646 | __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:6056:152: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 6056 | __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:6324:108: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 6324 | __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:6426:304: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 6426 | __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:8918:94: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 8918 | __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:8950:75: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 8950 | __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:8982:81: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 8982 | __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:9305:77: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 9305 | __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:9496:372: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 9496 | __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:9548:378: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 9548 | __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:9610:89: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 9610 | __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); | ^~ aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/bwlzh.o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/bwt.o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/coder.o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/dict.o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/fixpoint.o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/huffman.o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/huffmem.o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/lz77.o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/merge_sort.o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/mtf.o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/rle.o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/tng_compress.o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/vals16.o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/warnmalloc.o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/widemuldiv.o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/xtc2.o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/compression/xtc3.o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/lib/md5.o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/src/lib/tng_io.o build/temp.linux-aarch64-cpython-311/mdtraj/formats/tng/tng.o -L/usr/lib -L/usr/lib/aarch64-linux-gnu -lz -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/tng.cpython-311-aarch64-linux-gnu.so building 'mdtraj.formats.dcd' extension aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/dcd/dcd.c -o build/temp.linux-aarch64-cpython-311/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:1940, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/formats/dcd/dcd.c:782: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ In function '__Pyx_PyInt_From_int', inlined from '__pyx_pf_6mdtraj_7formats_3dcd_17DCDTrajectoryFile_20read' at mdtraj/formats/dcd/dcd.c:6646:17: mdtraj/formats/dcd/dcd.c:694:40: warning: '__pyx_v_i' may be used uninitialized [-Wmaybe-uninitialized] 694 | #define PyInt_FromLong PyLong_FromLong | ^ mdtraj/formats/dcd/dcd.c:13600:20: note: in expansion of macro 'PyInt_FromLong' 13600 | return PyInt_FromLong((long) value); | ^~~~~~~~~~~~~~ mdtraj/formats/dcd/dcd.c: In function '__pyx_pf_6mdtraj_7formats_3dcd_17DCDTrajectoryFile_20read': mdtraj/formats/dcd/dcd.c:5465:7: note: '__pyx_v_i' was declared here 5465 | int __pyx_v_i; | ^~~~~~~~~ aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/dcd/src/dcdplugin.c -o build/temp.linux-aarch64-cpython-311/mdtraj/formats/dcd/src/dcdplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-311/mdtraj/formats/dcd/dcd.o build/temp.linux-aarch64-cpython-311/mdtraj/formats/dcd/src/dcdplugin.o -L/usr/lib/aarch64-linux-gnu -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/dcd.cpython-311-aarch64-linux-gnu.so building 'mdtraj.formats.binpos' extension aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/binpos/binpos.c -o build/temp.linux-aarch64-cpython-311/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:1940, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/formats/binpos/binpos.c:782: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ In function '__pyx_pf_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_8_read', inlined from '__pyx_pw_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_9_read' at mdtraj/formats/binpos/binpos.c:4994:13: mdtraj/formats/binpos/binpos.c:5526:6: warning: '__pyx_v_status' may be used uninitialized [-Wmaybe-uninitialized] 5526 | if (__pyx_t_2) { | ^ mdtraj/formats/binpos/binpos.c: In function '__pyx_pw_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_9_read': mdtraj/formats/binpos/binpos.c:5006:7: note: '__pyx_v_status' was declared here 5006 | int __pyx_v_status; | ^~~~~~~~~~~~~~ In function '__Pyx_PyInt_From_int', inlined from '__pyx_pf_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_8_read' at mdtraj/formats/binpos/binpos.c:5536:17, inlined from '__pyx_pw_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_9_read' at mdtraj/formats/binpos/binpos.c:4994:13: mdtraj/formats/binpos/binpos.c:694:40: warning: '__pyx_v_i' may be used uninitialized [-Wmaybe-uninitialized] 694 | #define PyInt_FromLong PyLong_FromLong | ^ mdtraj/formats/binpos/binpos.c:13100:20: note: in expansion of macro 'PyInt_FromLong' 13100 | return PyInt_FromLong((long) value); | ^~~~~~~~~~~~~~ mdtraj/formats/binpos/binpos.c: In function '__pyx_pw_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_9_read': mdtraj/formats/binpos/binpos.c:5003:7: note: '__pyx_v_i' was declared here 5003 | int __pyx_v_i; | ^~~~~~~~~ aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.11 -c mdtraj/formats/binpos/src/binposplugin.c -o build/temp.linux-aarch64-cpython-311/mdtraj/formats/binpos/src/binposplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/formats/binpos/src/binposplugin.c: In function 'open_binpos_read': mdtraj/formats/binpos/src/binposplugin.c:59:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 59 | fread(magicchar,sizeof(char),4,fd); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/binpos/src/binposplugin.c:69:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 69 | fread(&igarb,sizeof(int),1,fd); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-311/mdtraj/formats/binpos/binpos.o build/temp.linux-aarch64-cpython-311/mdtraj/formats/binpos/src/binposplugin.o -L/usr/lib/aarch64-linux-gnu -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/binpos.cpython-311-aarch64-linux-gnu.so building 'mdtraj.formats.dtr' extension aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/dtr/dtr.cpp -o build/temp.linux-aarch64-cpython-311/mdtraj/formats/dtr/dtr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1940, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/formats/dtr/dtr.cpp:803: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/dtr/src/dtrplugin.cxx -o build/temp.linux-aarch64-cpython-311/mdtraj/formats/dtr/src/dtrplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ mdtraj/formats/dtr/src/dtrplugin.cxx: In member function 'bool desres::molfile::Timekeys::init(const std::string&)': mdtraj/formats/dtr/src/dtrplugin.cxx:487:27: warning: format '%d' expects argument of type 'int', but argument 2 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] 487 | printf("size %d framesize %d\n\n", | ~^ | | | int | %ld 488 | keys[i].size(), m_framesize); | ~~~~~~~~~~~~~~ | | | uint64_t {aka long unsigned int} mdtraj/formats/dtr/src/dtrplugin.cxx:487:40: warning: format '%d' expects argument of type 'int', but argument 3 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] 487 | printf("size %d framesize %d\n\n", | ~^ | | | int | %ld 488 | keys[i].size(), m_framesize); | ~~~~~~~~~~~ | | | uint64_t {aka long unsigned int} mdtraj/formats/dtr/src/dtrplugin.cxx: In constructor '{anonymous}::DDException::DDException(const std::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 std::string&, mode_t, int, int)': mdtraj/formats/dtr/src/dtrplugin.cxx:706:23: warning: '%03x' directive writing between 3 and 8 bytes into a region of size 6 [-Wformat-overflow=] 706 | sprintf(sub, "%03x/", i); | ^~~~ mdtraj/formats/dtr/src/dtrplugin.cxx:706:22: note: directive argument in the range [0, 2147483646] 706 | sprintf(sub, "%03x/", i); | ^~~~~~~ In file included from /usr/include/stdio.h:906, from mdtraj/formats/dtr/include/molfile_plugin.h:35, from mdtraj/formats/dtr/include/dtrplugin.hxx:46, from mdtraj/formats/dtr/src/dtrplugin.cxx:42: In function 'int sprintf(char*, const char*, ...)', inlined from 'void DDmkdir(const std::string&, mode_t, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:706:9: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 5 and 10 bytes into a destination of size 6 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ mdtraj/formats/dtr/src/dtrplugin.cxx: In function 'void DDmkdir(const std::string&, mode_t, int, int)': mdtraj/formats/dtr/src/dtrplugin.cxx:714:30: warning: '%03x' directive writing between 3 and 8 bytes into a region of size 6 [-Wformat-overflow=] 714 | sprintf(subsub, "%03x", j); | ^~~~ mdtraj/formats/dtr/src/dtrplugin.cxx:714:29: note: directive argument in the range [0, 2147483646] 714 | sprintf(subsub, "%03x", j); | ^~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'void DDmkdir(const std::string&, mode_t, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:714:13: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 4 and 9 bytes into a destination of size 6 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ mdtraj/formats/dtr/src/dtrplugin.cxx: In function 'std::string framefile(const std::string&, size_t, size_t, int, int)': mdtraj/formats/dtr/src/dtrplugin.cxx:667:35: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=] 667 | sprintf(answer, "%03x/", d1); | ^ In function 'int sprintf(char*, const char*, ...)', inlined from 'std::string DDreldir(const std::string&, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:667:13, inlined from 'std::string framefile(const std::string&, size_t, size_t, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:771:23: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 5 and 10 bytes into a destination of size 9 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ mdtraj/formats/dtr/src/dtrplugin.cxx: In function 'std::string framefile(const std::string&, size_t, size_t, int, int)': mdtraj/formats/dtr/src/dtrplugin.cxx:665:35: warning: '%03x' directive writing between 3 and 8 bytes into a region of size between 0 and 5 [-Wformat-overflow=] 665 | sprintf(answer, "%03x/%03x/", d1, d2); | ^~~~ In function 'std::string DDreldir(const std::string&, int, int)', inlined from 'std::string framefile(const std::string&, size_t, size_t, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:771:23: mdtraj/formats/dtr/src/dtrplugin.cxx:665:29: note: directive argument in the range [0, 2147483646] 665 | sprintf(answer, "%03x/%03x/", d1, d2); | ^~~~~~~~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'std::string DDreldir(const std::string&, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:665:13, inlined from 'std::string framefile(const std::string&, size_t, size_t, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:771:23: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 9 and 19 bytes into a destination of size 9 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-311/mdtraj/formats/dtr/dtr.o build/temp.linux-aarch64-cpython-311/mdtraj/formats/dtr/src/dtrplugin.o -L/usr/lib/aarch64-linux-gnu -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/dtr.cpython-311-aarch64-linux-gnu.so building 'mdtraj._rmsd' extension aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/rmsd/_rmsd.cpp -o build/temp.linux-aarch64-cpython-311/mdtraj/rmsd/_rmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-aarch64-cpython-311/mdtraj/rmsd/src/center.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/rmsd/src/rotation.cpp -o build/temp.linux-aarch64-cpython-311/mdtraj/rmsd/src/rotation.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-aarch64-cpython-311/mdtraj/rmsd/src/theobald_rmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-311/mdtraj/rmsd/_rmsd.o build/temp.linux-aarch64-cpython-311/mdtraj/rmsd/src/center.o build/temp.linux-aarch64-cpython-311/mdtraj/rmsd/src/rotation.o build/temp.linux-aarch64-cpython-311/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/_rmsd.cpython-311-aarch64-linux-gnu.so building 'mdtraj._lprmsd' extension aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/rmsd/_lprmsd.cpp -o build/temp.linux-aarch64-cpython-311/mdtraj/rmsd/_lprmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1940, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/rmsd/_lprmsd.cpp:812: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/rmsd/src/Munkres.cpp -o build/temp.linux-aarch64-cpython-311/mdtraj/rmsd/src/Munkres.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-aarch64-cpython-311/mdtraj/rmsd/src/center.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/rmsd/src/euclidean_permutation.cpp -o build/temp.linux-aarch64-cpython-311/mdtraj/rmsd/src/euclidean_permutation.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/rmsd/src/fancy_index.cpp -o build/temp.linux-aarch64-cpython-311/mdtraj/rmsd/src/fancy_index.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/rmsd/src/rotation.cpp -o build/temp.linux-aarch64-cpython-311/mdtraj/rmsd/src/rotation.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-aarch64-cpython-311/mdtraj/rmsd/src/theobald_rmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-311/mdtraj/rmsd/_lprmsd.o build/temp.linux-aarch64-cpython-311/mdtraj/rmsd/src/Munkres.o build/temp.linux-aarch64-cpython-311/mdtraj/rmsd/src/center.o build/temp.linux-aarch64-cpython-311/mdtraj/rmsd/src/euclidean_permutation.o build/temp.linux-aarch64-cpython-311/mdtraj/rmsd/src/fancy_index.o build/temp.linux-aarch64-cpython-311/mdtraj/rmsd/src/rotation.o build/temp.linux-aarch64-cpython-311/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/_lprmsd.cpython-311-aarch64-linux-gnu.so building 'mdtraj.geometry._geometry' extension aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/geometry/src/_geometry.cpp -o build/temp.linux-aarch64-cpython-311/mdtraj/geometry/src/_geometry.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1940, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/geometry/src/_geometry.cpp:814: /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:6129:277: warning: '__pyx_v_offset[1]' may be used uninitialized [-Wmaybe-uninitialized] 6129 | (__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:6035:9: note: '__pyx_v_offset[1]' was declared here 6035 | float __pyx_v_offset[3]; | ^~~~~~~~~~~~~~ mdtraj/geometry/src/_geometry.cpp:6129:277: warning: '__pyx_v_delta[1]' may be used uninitialized [-Wmaybe-uninitialized] 6129 | (__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:6036:9: note: '__pyx_v_delta[1]' was declared here 6036 | float __pyx_v_delta[3]; | ^~~~~~~~~~~~~ mdtraj/geometry/src/_geometry.cpp:6115:224: warning: '__pyx_v_delta[2]' may be used uninitialized [-Wmaybe-uninitialized] 6115 | (__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:6036:9: note: '__pyx_v_delta[2]' was declared here 6036 | float __pyx_v_delta[3]; | ^~~~~~~~~~~~~ aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/geometry/src/dssp.cpp -o build/temp.linux-aarch64-cpython-311/mdtraj/geometry/src/dssp.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/geometry/src/geometry.cpp -o build/temp.linux-aarch64-cpython-311/mdtraj/geometry/src/geometry.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/geometry/src/sasa.cpp -o build/temp.linux-aarch64-cpython-311/mdtraj/geometry/src/sasa.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-311/mdtraj/geometry/src/_geometry.o build/temp.linux-aarch64-cpython-311/mdtraj/geometry/src/dssp.o build/temp.linux-aarch64-cpython-311/mdtraj/geometry/src/geometry.o build/temp.linux-aarch64-cpython-311/mdtraj/geometry/src/sasa.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/_geometry.cpython-311-aarch64-linux-gnu.so building 'mdtraj.geometry.drid' extension aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/geometry/drid.cpp -o build/temp.linux-aarch64-cpython-311/mdtraj/geometry/drid.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/geometry/src/dridkernels.cpp -o build/temp.linux-aarch64-cpython-311/mdtraj/geometry/src/dridkernels.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/geometry/src/moments.cpp -o build/temp.linux-aarch64-cpython-311/mdtraj/geometry/src/moments.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-311/mdtraj/geometry/drid.o build/temp.linux-aarch64-cpython-311/mdtraj/geometry/src/dridkernels.o build/temp.linux-aarch64-cpython-311/mdtraj/geometry/src/moments.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/drid.cpython-311-aarch64-linux-gnu.so building 'mdtraj.geometry.neighbors' extension aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/geometry/neighbors.cpp -o build/temp.linux-aarch64-cpython-311/mdtraj/geometry/neighbors.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/geometry/src/neighbors.cpp -o build/temp.linux-aarch64-cpython-311/mdtraj/geometry/src/neighbors.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-311/mdtraj/geometry/neighbors.o build/temp.linux-aarch64-cpython-311/mdtraj/geometry/src/neighbors.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/neighbors.cpython-311-aarch64-linux-gnu.so building 'mdtraj.geometry.neighborlist' extension aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/geometry/neighborlist.cpp -o build/temp.linux-aarch64-cpython-311/mdtraj/geometry/neighborlist.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/geometry/src/neighborlist.cpp -o build/temp.linux-aarch64-cpython-311/mdtraj/geometry/src/neighborlist.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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:51:53: warning: 'periodicBoxVectors' may be used uninitialized [-Wmaybe-uninitialized] 51 | periodicBoxSize[1] = periodicBoxVectors[1][1]; | ~~~~~~~~~~~~~~~~~~~~~~~^ 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:52:53: warning: 'periodicBoxVectors' may be used uninitialized [-Wmaybe-uninitialized] 52 | periodicBoxSize[2] = periodicBoxVectors[2][2]; | ~~~~~~~~~~~~~~~~~~~~~~~^ 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]; | ^~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-311/mdtraj/geometry/neighborlist.o build/temp.linux-aarch64-cpython-311/mdtraj/geometry/src/neighborlist.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/neighborlist.cpython-311-aarch64-linux-gnu.so running install_lib creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11 creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/_lprmsd.cpython-311-aarch64-linux-gnu.so -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/_rmsd.cpython-311-aarch64-linux-gnu.so -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/version.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/__pycache__/version.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/__pycache__/__init__.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/__pycache__ creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core/__pycache__/trajectory.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core/__pycache__/selection.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core/__pycache__/residue_names.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core/__pycache__/topology.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core/__pycache__/element.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core/__pycache__/__init__.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core/__pycache__ creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core/lib copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core/lib/center.h -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core/lib copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core/lib/theobald_rmsd.h -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core/lib copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core/lib/libtheobald.a -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core/lib copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core/__init__.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core/element.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core/residue_names.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core/selection.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core/topology.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core/trajectory.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/dtr.cpython-311-aarch64-linux-gnu.so -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/binpos.cpython-311-aarch64-linux-gnu.so -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/dcd.cpython-311-aarch64-linux-gnu.so -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/tng.cpython-311-aarch64-linux-gnu.so -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/trr.cpython-311-aarch64-linux-gnu.so -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/xtc.cpython-311-aarch64-linux-gnu.so -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/__pycache__/gsd.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/__pycache__/hoomdxml.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/__pycache__/mol2.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/__pycache__/psf.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/__pycache__/prmtop.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/__pycache__/openmmxml.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/__pycache__/pdbx.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/__pycache__/xyzfile.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/__pycache__/gro.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/__pycache__/lammpstrj.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/__pycache__/amberrst.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/__pycache__/mdcrd.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/__pycache__/lh5.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/__pycache__/netcdf.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/__pycache__/hdf5.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/__pycache__/registry.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/__pycache__/arc.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/__pycache__/__init__.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/__pycache__ creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/pdb creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/pdb/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/pdb/__pycache__/pdbstructure.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/pdb/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/pdb/__pycache__/pdbfile.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/pdb/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/pdb/__pycache__/__init__.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/pdb/__pycache__ creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/pdb/data copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/pdb/data/pdbNames.xml -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/pdb/data copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/pdb/data/residues.xml -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/pdb/data copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/pdb/__init__.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/pdb copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/pdb/pdbfile.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/pdb copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/pdb/pdbstructure.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/pdb copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/__init__.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/amberrst.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/arc.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/gro.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/gsd.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/hdf5.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/hoomdxml.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/lammpstrj.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/lh5.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/mdcrd.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/mol2.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/netcdf.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/openmmxml.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/pdbx.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/prmtop.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/psf.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/registry.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/xyzfile.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/neighborlist.cpython-311-aarch64-linux-gnu.so -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/neighbors.cpython-311-aarch64-linux-gnu.so -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/drid.cpython-311-aarch64-linux-gnu.so -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/_geometry.cpython-311-aarch64-linux-gnu.so -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/__pycache__/shape.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/__pycache__/order.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/__pycache__/rdf.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/__pycache__/thermodynamic_properties.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/__pycache__/dssp.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/__pycache__/contact.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/__pycache__/sasa.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/__pycache__/hbond.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/__pycache__/dihedral.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/__pycache__/distance.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/__pycache__/angle.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/__pycache__/rg.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/__pycache__/__init__.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/__init__.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/alignment.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/angle.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/contact.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/dihedral.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/distance.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/dssp.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/hbond.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/internal.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/order.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/rdf.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/rg.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/sasa.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/shape.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/thermodynamic_properties.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/nmr creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/nmr/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/nmr/__pycache__/scalar_couplings.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/nmr/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/nmr/__pycache__/shift_wrappers.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/nmr/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/nmr/__pycache__/__init__.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/nmr/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/nmr/__init__.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/nmr copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/nmr/scalar_couplings.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/nmr copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/nmr/shift_wrappers.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/nmr creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/reporters creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/reporters/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/reporters/__pycache__/xtcreporter.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/reporters/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/reporters/__pycache__/dcdreporter.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/reporters/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/reporters/__pycache__/netcdfreporter.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/reporters/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/reporters/__pycache__/basereporter.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/reporters/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/reporters/__pycache__/hdf5reporter.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/reporters/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/reporters/__pycache__/__init__.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/reporters/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/reporters/__init__.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/reporters copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/reporters/basereporter.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/reporters copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/reporters/dcdreporter.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/reporters copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/reporters/hdf5reporter.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/reporters copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/reporters/netcdfreporter.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/reporters copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/reporters/xtcreporter.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/reporters creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/scripts creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/scripts/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/scripts/__pycache__/__init__.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/scripts/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/scripts/__init__.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/scripts copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/scripts/mdconvert.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/scripts copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/scripts/mdinspect.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/scripts creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/testing creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/testing/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/testing/__pycache__/docscrape.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/testing/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/testing/__pycache__/docstrings.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/testing/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/testing/__pycache__/testing.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/testing/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/testing/__pycache__/__init__.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/testing/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/testing/__init__.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/testing copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/testing/docscrape.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/testing copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/testing/docstrings.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/testing copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/testing/testing.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/testing creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/__pycache__/singleton.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/__pycache__/zipped.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/__pycache__/contextmanagers.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/__pycache__/unitcell.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/__pycache__/rotation.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/__pycache__/six.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/__pycache__/validation.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/__pycache__/delay_import.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/__pycache__/__init__.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/__pycache__ creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/__pycache__/prefix.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/__pycache__/unit_operators.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/__pycache__/unit_definitions.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/__pycache__/baseunit.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/__pycache__/mymatrix.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/__pycache__/unit.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/__pycache__/basedimension.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/__pycache__/standard_dimensions.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/__pycache__/quantity.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/__pycache__/__init__.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/__init__.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/mymatrix.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/constants.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/prefix.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/quantity.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/standard_dimensions.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/unit_definitions.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/unit_math.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/unit_operators.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/basedimension.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/baseunit.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/doctests.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/unit.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/__init__.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/contextmanagers.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/delay_import.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/rotation.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/singleton.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/six.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unitcell.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/validation.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/zipped.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/__init__.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/io.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/version.py to version.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core/__init__.py to __init__.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core/element.py to element.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core/residue_names.py to residue_names.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core/selection.py to selection.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core/topology.py to topology.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core/trajectory.py to trajectory.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/pdb/__init__.py to __init__.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/pdb/pdbfile.py to pdbfile.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/pdb/pdbstructure.py to pdbstructure.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/__init__.py to __init__.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/amberrst.py to amberrst.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/arc.py to arc.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/gro.py to gro.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/gsd.py to gsd.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/hdf5.py to hdf5.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/hoomdxml.py to hoomdxml.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/lammpstrj.py to lammpstrj.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/lh5.py to lh5.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/mdcrd.py to mdcrd.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/mol2.py to mol2.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/netcdf.py to netcdf.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/openmmxml.py to openmmxml.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/pdbx.py to pdbx.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/prmtop.py to prmtop.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/psf.py to psf.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/registry.py to registry.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/xyzfile.py to xyzfile.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/__init__.py to __init__.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/alignment.py to alignment.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/angle.py to angle.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/contact.py to contact.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/dihedral.py to dihedral.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/distance.py to distance.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/dssp.py to dssp.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/hbond.py to hbond.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/internal.py to internal.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/order.py to order.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/rdf.py to rdf.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/rg.py to rg.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/sasa.py to sasa.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/shape.py to shape.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/thermodynamic_properties.py to thermodynamic_properties.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/nmr/__init__.py to __init__.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/nmr/scalar_couplings.py to scalar_couplings.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/nmr/shift_wrappers.py to shift_wrappers.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/reporters/__init__.py to __init__.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/reporters/basereporter.py to basereporter.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/reporters/dcdreporter.py to dcdreporter.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/reporters/hdf5reporter.py to hdf5reporter.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/reporters/netcdfreporter.py to netcdfreporter.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/reporters/xtcreporter.py to xtcreporter.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/scripts/__init__.py to __init__.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/scripts/mdconvert.py to mdconvert.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/scripts/mdinspect.py to mdinspect.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/testing/__init__.py to __init__.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/testing/docscrape.py to docscrape.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/testing/docstrings.py to docstrings.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/testing/testing.py to testing.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit/__init__.py to __init__.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit/mymatrix.py to mymatrix.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit/constants.py to constants.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit/prefix.py to prefix.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit/quantity.py to quantity.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit/standard_dimensions.py to standard_dimensions.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit/unit_definitions.py to unit_definitions.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit/unit_math.py to unit_math.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit/unit_operators.py to unit_operators.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit/basedimension.py to basedimension.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit/baseunit.py to baseunit.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit/doctests.py to doctests.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit/unit.py to unit.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/__init__.py to __init__.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/contextmanagers.py to contextmanagers.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/delay_import.py to delay_import.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/rotation.py to rotation.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/singleton.py to singleton.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/six.py to six.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unitcell.py to unitcell.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/validation.py to validation.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/zipped.py to zipped.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/__init__.py to __init__.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/io.py to io.cpython-311.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 dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative reading manifest file 'mdtraj.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' no previously-included directories found matching '__pycache__' no previously-included directories found matching '*.pyc' adding license file 'LICENSE' writing manifest file 'mdtraj.egg-info/SOURCES.txt' Copying mdtraj.egg-info to /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj-1.9.9.egg-info Skipping SOURCES.txt running install_scripts Installing mdconvert-mdtraj script to /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/bin Installing mdinspect script to /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/bin dh_install -O--buildsystem=pybuild install -m0755 -d debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples/data cp --reflink=auto -a ./debian/external/2EQQ.pdb ./debian/external/2MI7.pdb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples/data/ install -m0755 -d debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/doi-10.1016_j.bpj.2015.08.015-blue.svg cp --reflink=auto -a ./debian/external/doi-10.1016_j.bpj.2015.08.015-blue.svg debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/doi-10.1016_j.bpj.2015.08.015-blue.svg/ dh_installdocs -O--buildsystem=pybuild dh_installdocs: warning: Cannot auto-detect main package for python-mdtraj-doc. If the default is wrong, please use --doc-main-package install -m0755 -d debian/python3-mdtraj/usr/share/doc/python3-mdtraj install -p -m0644 debian/copyright debian/python3-mdtraj/usr/share/doc/python3-mdtraj/copyright install -m0755 -d debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc cd './build/html/..' && find 'html' \( -type f -or -type l \) -and ! -empty -print0 | LC_ALL=C sort -z | xargs -0 -I {} cp --reflink=auto --parents -dp {} /build/reproducible-path/mdtraj-1.9.9/debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc cp --reflink=auto -a ./README.md debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc chmod -R u\+rw,go=rX debian/python-mdtraj-doc/usr/share/doc install -p -m0644 debian/copyright debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/copyright install -m0755 -d debian/python-mdtraj-doc/usr/share/doc-base/ install -p -m0644 debian/python-mdtraj-doc.doc-base debian/python-mdtraj-doc/usr/share/doc-base/python-mdtraj-doc.mdtraj rm -f debian/python-mdtraj-doc.debhelper.log debian/rules override_dh_sphinxdoc-indep make[1]: Entering directory '/build/reproducible-path/mdtraj-1.9.9' dh_sphinxdoc -i ln -sf ../../../../../sphinx_rtd_theme/static/js/theme.js debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/js/theme.js ln -sf ../../../../../sphinx_rtd_theme/static/fonts/fontawesome-webfont.woff2 debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.woff2 ln -sf ../../../../../sphinx_rtd_theme/static/fonts/fontawesome-webfont.woff debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.woff ln -sf ../../../../../sphinx_rtd_theme/static/fonts/fontawesome-webfont.ttf debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.ttf ln -sf ../../../../../sphinx_rtd_theme/static/fonts/fontawesome-webfont.svg debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.svg ln -sf ../../../../../sphinx_rtd_theme/static/fonts/fontawesome-webfont.eot debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.eot ln -sf ../../../../../sphinx_rtd_theme/static/fonts/Lato-Regular.ttf debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Regular.ttf ln -sf ../../../../../sphinx_rtd_theme/static/fonts/Lato-Italic.ttf debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Italic.ttf ln -sf ../../../../../sphinx_rtd_theme/static/fonts/Lato-BoldItalic.ttf debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-BoldItalic.ttf ln -sf ../../../../../sphinx_rtd_theme/static/fonts/Lato-Bold.ttf debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Bold.ttf ln -sf ../../../../../sphinx_rtd_theme/static/fonts/RobotoSlab-Regular.woff2 debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/RobotoSlab-Regular.woff2 ln -sf ../../../../../sphinx_rtd_theme/static/fonts/RobotoSlab-Bold.woff2 debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/RobotoSlab-Bold.woff2 ln -sf ../../../../../sphinx_rtd_theme/static/fonts/Lato-Regular.woff2 debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Regular.woff2 ln -sf ../../../../../sphinx_rtd_theme/static/fonts/Lato-Italic.woff2 debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Italic.woff2 ln -sf ../../../../../sphinx_rtd_theme/static/fonts/Lato-BoldItalic.woff2 debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-BoldItalic.woff2 ln -sf ../../../../../sphinx_rtd_theme/static/fonts/Lato-Bold.woff2 debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Bold.woff2 ln -sf ../../../../../sphinx_rtd_theme/static/css/theme.css debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/css/theme.css ln -sf ../../../../../sphinx_rtd_theme/static/css/badge_only.css debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/css/badge_only.css ln -sf ../../../../javascript/sphinxdoc/1.0/searchtools.js debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/searchtools.js ln -sf ../../../../javascript/sphinxdoc/1.0/language_data.js debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/language_data.js ln -sf ../../../../javascript/sphinxdoc/1.0/sphinx_highlight.js debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/sphinx_highlight.js dh_sphinxdoc: warning: ignoring unknown JavaScript code: debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/js/versions.js ln -sf ../../../../javascript/sphinxdoc/1.0/doctools.js debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/doctools.js rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/.buildinfo mv debian/python-mdtraj-doc.substvars.new debian/python-mdtraj-doc.substvars mv debian/python-mdtraj-doc.substvars.new debian/python-mdtraj-doc.substvars mv debian/python-mdtraj-doc.substvars.new debian/python-mdtraj-doc.substvars mv debian/python-mdtraj-doc.substvars.new debian/python-mdtraj-doc.substvars mv debian/python-mdtraj-doc.substvars.new debian/python-mdtraj-doc.substvars sed "s|src=\"https://img.shields.io/badge/DOI-10.1016%2Fj.bpj.2015.08.015-blue.svg\"|src=\"_static/doi-10.1016_j.bpj.2015.08.015-blue.svg\"|g" -i debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/index.html make[1]: Leaving directory '/build/reproducible-path/mdtraj-1.9.9' dh_sphinxdoc -O--buildsystem=pybuild -Npython-mdtraj-doc dh_sphinxdoc: warning: Sphinx documentation not found dh_installchangelogs -O--buildsystem=pybuild install -m0755 -d debian/python3-mdtraj/usr/share/doc/python3-mdtraj install -p -m0644 debian/.debhelper/generated/python3-mdtraj/dh_installchangelogs.dch.trimmed debian/python3-mdtraj/usr/share/doc/python3-mdtraj/changelog.Debian install -m0755 -d debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc install -p -m0644 debian/.debhelper/generated/python-mdtraj-doc/dh_installchangelogs.dch.trimmed debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/changelog.Debian dh_installexamples -O--buildsystem=pybuild dh_installexamples: warning: Cannot auto-detect main package for python-mdtraj-doc. If the default is wrong, please use --doc-main-package install -m0755 -d debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples cp --reflink=auto -a ./examples/1vii_3frames.pdb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples cp --reflink=auto -a ./examples/ala2.h5 debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples cp --reflink=auto -a ./examples/atom-selection.ipynb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples cp --reflink=auto -a ./examples/centroids.ipynb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples cp --reflink=auto -a ./examples/clustering.ipynb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples cp --reflink=auto -a ./examples/data debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples cp --reflink=auto -a ./examples/hbonds.ipynb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples cp --reflink=auto -a ./examples/iterload.ipynb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples cp --reflink=auto -a ./examples/native-contact.ipynb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples cp --reflink=auto -a ./examples/nmr.ipynb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples cp --reflink=auto -a ./examples/principal-components.ipynb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples cp --reflink=auto -a ./examples/ramachandran-plot.ipynb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples cp --reflink=auto -a ./examples/rmsd-benchmark.ipynb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples cp --reflink=auto -a ./examples/rmsd-drift.ipynb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples cp --reflink=auto -a ./examples/simulation-with-openmm.ipynb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples cp --reflink=auto -a ./examples/solvent-accessible-surface-area.ipynb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples cp --reflink=auto -a ./examples/test_examples.py debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples cp --reflink=auto -a ./examples/two-pass-clustering.ipynb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples dh_installman -O--buildsystem=pybuild install -m0755 -d debian/python3-mdtraj/usr/share/man/man1/ install -p -m0644 ./debian/mdconvert-mdtraj.1 debian/python3-mdtraj/usr/share/man/man1/mdconvert-mdtraj.1 install -m0755 -d debian/python3-mdtraj/usr/share/man/man1/ install -p -m0644 ./debian/mdinspect.1 debian/python3-mdtraj/usr/share/man/man1/mdinspect.1 man-recode --to-code UTF-8 --suffix .dh-new debian/python3-mdtraj/usr/share/man/man1/mdconvert-mdtraj.1 man-recode --to-code UTF-8 --suffix .dh-new debian/python3-mdtraj/usr/share/man/man1/mdinspect.1 mv debian/python3-mdtraj/usr/share/man/man1/mdconvert-mdtraj.1.dh-new debian/python3-mdtraj/usr/share/man/man1/mdconvert-mdtraj.1 chmod 0644 -- debian/python3-mdtraj/usr/share/man/man1/mdconvert-mdtraj.1 mv debian/python3-mdtraj/usr/share/man/man1/mdinspect.1.dh-new debian/python3-mdtraj/usr/share/man/man1/mdinspect.1 chmod 0644 -- debian/python3-mdtraj/usr/share/man/man1/mdinspect.1 rm -f debian/python-mdtraj-doc.debhelper.log debian/rules override_dh_python3 make[1]: Entering directory '/build/reproducible-path/mdtraj-1.9.9' dh_python3 D: dh_python3 dh_python3:179: version: 6.20240422 D: dh_python3 dh_python3:180: argv: ['/usr/bin/dh_python3'] D: dh_python3 dh_python3:181: options: Namespace(guess_deps=True, skip_private=False, verbose=True, arch=None, package=None, no_package=None, remaining_packages=False, compile_all=False, vrange=None, regexpr=None, accept_upstream_versions=False, depends=None, depends_section=None, recommends=None, recommends_section=None, suggests=None, suggests_section=None, requires=None, shebang=None, ignore_shebangs=False, clean_dbg_pkg=True, no_ext_rename=False, no_shebang_rewrite=False, private_dir=None, O=None) D: dh_python3 dh_python3:182: supported Python versions: 3.11,3.12 (default=3.11) D: dh_python3 debhelper:166: skipping package python-mdtraj-doc (missing ${python3:Depends} in Depends/Recommends) D: dh_python3 debhelper:174: source=mdtraj, binary packages=['python3-mdtraj'] D: dh_python3 dh_python3:204: processing package python3-mdtraj... D: dh_python3 fs:50: moving files from debian/python3-mdtraj/usr/lib/python3.11/dist-packages to debian/python3-mdtraj/usr/lib/python3/dist-packages/ D: dh_python3 fs:50: moving files from debian/python3-mdtraj/usr/lib/python3.12/dist-packages to debian/python3-mdtraj/usr/lib/python3/dist-packages/ W: dh_python3 fs:122: Paths differ: debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/lib/libtheobald.a and debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/core/lib/libtheobald.a D: dh_python3 fs:335: package python3-mdtraj details = {'requires.txt': {'debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj-1.9.9.egg-info/requires.txt'}, 'egg-info': {'debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj-1.9.9.egg-info/PKG-INFO'}, 'dist-info': set(), 'nsp.txt': set(), 'shebangs': {/usr/bin/python3, /usr/bin/python3}, 'public_vers': {Version('3'), Version('3.12')}, 'private_dirs': {}, 'compile': True, 'ext_vers': {Version('3.11'), Version('3.12')}, 'ext_no_version': set()} D: dh_python3 depends:103: generating dependencies for package python3-mdtraj D: dh_python3 pydist:173: trying to find dependency for astunparse (python=None) D: dh_python3 pydist:207: dependency: module seems to be installed D: dh_python3 pydist:270: dependency: included in build-deps D: dh_python3 pydist:173: trying to find dependency for numpy>=1.6 (python=None) D: dh_python3 pydist:207: dependency: module seems to be installed D: dh_python3 pydist:270: dependency: included in build-deps D: dh_python3 pydist:173: trying to find dependency for pyparsing (python=None) D: dh_python3 pydist:207: dependency: module seems to be installed D: dh_python3 pydist:270: dependency: included in build-deps D: dh_python3 pydist:173: trying to find dependency for scipy (python=None) D: dh_python3 pydist:207: dependency: module seems to be installed D: dh_python3 pydist:270: dependency: included in build-deps D: dh_python3 depends:253: D={'python3-astunparse', 'python3 (<< 3.13)', 'python3:any', 'python3-pyparsing', 'python3-scipy', 'python3-numpy', 'python3 (>= 3.11~)'}; R=[]; S=[]; E=[], B=[]; RT=[] dh_numpy3 mv debian/python3-mdtraj.substvars.new debian/python3-mdtraj.substvars mv debian/python-mdtraj-doc.substvars.new debian/python-mdtraj-doc.substvars # FIXME: No idea why a copy of this static lib (is it needed at all???) remains here. There is another one in usr/lib/python3/dist-packages rm -f debian/python3-mdtraj/usr/lib/python3.1*/dist-packages/mdtraj/core/lib/libtheobald.a make[1]: Leaving directory '/build/reproducible-path/mdtraj-1.9.9' dh_installsystemduser -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/css/theme.css ln -s ../../../../../sphinx_rtd_theme/static/css/theme.css debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/css/theme.css rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/css/badge_only.css ln -s ../../../../../sphinx_rtd_theme/static/css/badge_only.css debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/css/badge_only.css rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.woff2 ln -s ../../../../../sphinx_rtd_theme/static/fonts/fontawesome-webfont.woff2 debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.woff2 rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.woff ln -s ../../../../../sphinx_rtd_theme/static/fonts/fontawesome-webfont.woff debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.woff rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.ttf ln -s ../../../../../sphinx_rtd_theme/static/fonts/fontawesome-webfont.ttf debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.ttf rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.svg ln -s ../../../../../sphinx_rtd_theme/static/fonts/fontawesome-webfont.svg debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.svg rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.eot ln -s ../../../../../sphinx_rtd_theme/static/fonts/fontawesome-webfont.eot debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.eot rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Regular.ttf ln -s ../../../../../sphinx_rtd_theme/static/fonts/Lato-Regular.ttf debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Regular.ttf rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Italic.ttf ln -s ../../../../../sphinx_rtd_theme/static/fonts/Lato-Italic.ttf debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Italic.ttf rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-BoldItalic.ttf ln -s ../../../../../sphinx_rtd_theme/static/fonts/Lato-BoldItalic.ttf debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-BoldItalic.ttf rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Bold.ttf ln -s ../../../../../sphinx_rtd_theme/static/fonts/Lato-Bold.ttf debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Bold.ttf rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/RobotoSlab-Regular.woff2 ln -s ../../../../../sphinx_rtd_theme/static/fonts/RobotoSlab-Regular.woff2 debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/RobotoSlab-Regular.woff2 rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/RobotoSlab-Bold.woff2 ln -s ../../../../../sphinx_rtd_theme/static/fonts/RobotoSlab-Bold.woff2 debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/RobotoSlab-Bold.woff2 rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Regular.woff2 ln -s ../../../../../sphinx_rtd_theme/static/fonts/Lato-Regular.woff2 debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Regular.woff2 rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Italic.woff2 ln -s ../../../../../sphinx_rtd_theme/static/fonts/Lato-Italic.woff2 debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Italic.woff2 rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-BoldItalic.woff2 ln -s ../../../../../sphinx_rtd_theme/static/fonts/Lato-BoldItalic.woff2 debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-BoldItalic.woff2 rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Bold.woff2 ln -s ../../../../../sphinx_rtd_theme/static/fonts/Lato-Bold.woff2 debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Bold.woff2 rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/js/theme.js ln -s ../../../../../sphinx_rtd_theme/static/js/theme.js debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/js/theme.js rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/searchtools.js ln -s ../../../../javascript/sphinxdoc/1.0/searchtools.js debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/searchtools.js rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/language_data.js ln -s ../../../../javascript/sphinxdoc/1.0/language_data.js debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/language_data.js rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/sphinx_highlight.js ln -s ../../../../javascript/sphinxdoc/1.0/sphinx_highlight.js debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/sphinx_highlight.js rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/doctools.js ln -s ../../../../javascript/sphinxdoc/1.0/doctools.js debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/doctools.js dh_strip_nondeterminism -O--buildsystem=pybuild Using 1705400061 as canonical time Normalizing debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/plus.png using File::StripNondeterminism::handlers::png Normalizing debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/minus.png using File::StripNondeterminism::handlers::png Normalizing debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/file.png using File::StripNondeterminism::handlers::png Normalizing debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/mdtraj_logo-small.png using File::StripNondeterminism::handlers::png dh_compress -O--buildsystem=pybuild cd debian/python3-mdtraj cd debian/python-mdtraj-doc chmod a-x usr/share/doc/python3-mdtraj/changelog.Debian usr/share/man/man1/mdconvert-mdtraj.1 usr/share/man/man1/mdinspect.1 chmod a-x usr/share/doc/python-mdtraj-doc/changelog.Debian usr/share/doc/python-mdtraj-doc/html/_static/example-trajectoryview-data.json usr/share/doc/python-mdtraj-doc/html/_static/mdtraj_logo.xcf gzip -9nf usr/share/doc/python3-mdtraj/changelog.Debian usr/share/man/man1/mdconvert-mdtraj.1 usr/share/man/man1/mdinspect.1 gzip -9nf usr/share/doc/python-mdtraj-doc/changelog.Debian usr/share/doc/python-mdtraj-doc/html/_static/example-trajectoryview-data.json usr/share/doc/python-mdtraj-doc/html/_static/mdtraj_logo.xcf cd '/build/reproducible-path/mdtraj-1.9.9' cd '/build/reproducible-path/mdtraj-1.9.9' dh_fixperms -O--buildsystem=pybuild find debian/python3-mdtraj ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/python-mdtraj-doc ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/python-mdtraj-doc/usr/share/doc -type f -a -true -a ! -regex 'debian/python-mdtraj-doc/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/python3-mdtraj/usr/share/doc -type f -a -true -a ! -regex 'debian/python3-mdtraj/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/python-mdtraj-doc/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/python-mdtraj-doc -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/python3-mdtraj/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/python3-mdtraj/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/python3-mdtraj -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/python3-mdtraj/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x find debian/python3-mdtraj/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w dh_missing -O--buildsystem=pybuild dh_dwz -a -O--buildsystem=pybuild install -m0755 -d debian/python3-mdtraj/usr/lib/debug/.dwz/aarch64-linux-gnu dwz -mdebian/python3-mdtraj/usr/lib/debug/.dwz/aarch64-linux-gnu/python3-mdtraj.debug -M/usr/lib/debug/.dwz/aarch64-linux-gnu/python3-mdtraj.debug -- debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_lprmsd.cpython-311-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_lprmsd.cpython-312-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_rmsd.cpython-311-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_rmsd.cpython-312-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/binpos.cpython-311-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/binpos.cpython-312-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dcd.cpython-311-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dcd.cpython-312-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dtr.cpython-311-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dtr.cpython-312-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/tng.cpython-311-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/tng.cpython-312-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/trr.cpython-311-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/trr.cpython-312-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/xtc.cpython-311-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/xtc.cpython-312-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/_geometry.cpython-311-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/_geometry.cpython-312-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/drid.cpython-311-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/drid.cpython-312-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighborlist.cpython-311-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighborlist.cpython-312-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighbors.cpython-311-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighbors.cpython-312-aarch64-linux-gnu.so objcopy --compress-debug-sections debian/python3-mdtraj/usr/lib/debug/.dwz/aarch64-linux-gnu/python3-mdtraj.debug chmod 0644 -- debian/python3-mdtraj/usr/lib/debug/.dwz/aarch64-linux-gnu/python3-mdtraj.debug dh_strip -a -O--buildsystem=pybuild install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/25 objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_rmsd.cpython-312-aarch64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/25/ec669c9693bdda7b7b2869026df91dbf75fb27.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/25/ec669c9693bdda7b7b2869026df91dbf75fb27.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_rmsd.cpython-312-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/25/ec669c9693bdda7b7b2869026df91dbf75fb27.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_rmsd.cpython-312-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/b2 objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_rmsd.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/b2/ce5bb391bff5ea7af7c4a8e65deae8b40a136e.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/b2/ce5bb391bff5ea7af7c4a8e65deae8b40a136e.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_rmsd.cpython-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/b2/ce5bb391bff5ea7af7c4a8e65deae8b40a136e.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_rmsd.cpython-311-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/28 objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_lprmsd.cpython-312-aarch64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/28/28dc983153d150fc070173a098386362d964c4.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/28/28dc983153d150fc070173a098386362d964c4.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_lprmsd.cpython-312-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/28/28dc983153d150fc070173a098386362d964c4.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_lprmsd.cpython-312-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/2f objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_lprmsd.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/2f/0bc8f8923e8272f7723445cada8ab49413817a.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/2f/0bc8f8923e8272f7723445cada8ab49413817a.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_lprmsd.cpython-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/2f/0bc8f8923e8272f7723445cada8ab49413817a.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_lprmsd.cpython-311-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/6e objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dtr.cpython-312-aarch64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/6e/7df4bccb447cef575158ccd534c5564fa8a273.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/6e/7df4bccb447cef575158ccd534c5564fa8a273.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dtr.cpython-312-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/6e/7df4bccb447cef575158ccd534c5564fa8a273.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dtr.cpython-312-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/6a objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/xtc.cpython-312-aarch64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/6a/3205ed0388d44b4c1e2ad7d4e7e1e9d41ace84.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/6a/3205ed0388d44b4c1e2ad7d4e7e1e9d41ace84.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/xtc.cpython-312-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/6a/3205ed0388d44b4c1e2ad7d4e7e1e9d41ace84.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/xtc.cpython-312-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/30 objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/xtc.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/30/a547a8931b707ad5e76d427c7be844910f17e2.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/30/a547a8931b707ad5e76d427c7be844910f17e2.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/xtc.cpython-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/30/a547a8931b707ad5e76d427c7be844910f17e2.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/xtc.cpython-311-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/73 objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/tng.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/73/5aa1afe088160437b05ee8c737be6107b020fe.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/73/5aa1afe088160437b05ee8c737be6107b020fe.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/tng.cpython-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/73/5aa1afe088160437b05ee8c737be6107b020fe.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/tng.cpython-311-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/dd objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/tng.cpython-312-aarch64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/dd/c1a6f731b4ff4e0e89198c0405fb943c207ffe.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/dd/c1a6f731b4ff4e0e89198c0405fb943c207ffe.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/tng.cpython-312-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/dd/c1a6f731b4ff4e0e89198c0405fb943c207ffe.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/tng.cpython-312-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/71 objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dtr.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/71/6ddafa19c853611670dcfecda6efbec3e6bbff.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/71/6ddafa19c853611670dcfecda6efbec3e6bbff.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dtr.cpython-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/71/6ddafa19c853611670dcfecda6efbec3e6bbff.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dtr.cpython-311-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/df objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/trr.cpython-312-aarch64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/df/e184c717f6d8ae87fc563bb6589c4c85cf6578.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/df/e184c717f6d8ae87fc563bb6589c4c85cf6578.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/trr.cpython-312-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/df/e184c717f6d8ae87fc563bb6589c4c85cf6578.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/trr.cpython-312-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/36 objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/trr.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/36/4fe6512e3f023d8c9b3688037312c48d6e4820.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/36/4fe6512e3f023d8c9b3688037312c48d6e4820.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/trr.cpython-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/36/4fe6512e3f023d8c9b3688037312c48d6e4820.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/trr.cpython-311-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/06 objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dcd.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/06/49067756663be460c738d4e8284ea0ecd87375.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/06/49067756663be460c738d4e8284ea0ecd87375.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dcd.cpython-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/06/49067756663be460c738d4e8284ea0ecd87375.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dcd.cpython-311-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/49 objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dcd.cpython-312-aarch64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/49/9b3b1aedc1aced6a292c1006726a66ad9f1e06.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/49/9b3b1aedc1aced6a292c1006726a66ad9f1e06.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dcd.cpython-312-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/49/9b3b1aedc1aced6a292c1006726a66ad9f1e06.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dcd.cpython-312-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/cd objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/binpos.cpython-312-aarch64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/cd/5f0de02111520c5fb18a88ed2822fc2d08e571.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/cd/5f0de02111520c5fb18a88ed2822fc2d08e571.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/binpos.cpython-312-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/cd/5f0de02111520c5fb18a88ed2822fc2d08e571.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/binpos.cpython-312-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/f6 objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/binpos.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/f6/d9895d1c7c2f3d41a8259129d34863a1848ad3.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/f6/d9895d1c7c2f3d41a8259129d34863a1848ad3.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/binpos.cpython-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/f6/d9895d1c7c2f3d41a8259129d34863a1848ad3.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/binpos.cpython-311-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/d0 objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/_geometry.cpython-312-aarch64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/d0/88c988ab0db6d1db34e97f066b94938568c1a8.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/d0/88c988ab0db6d1db34e97f066b94938568c1a8.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/_geometry.cpython-312-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/d0/88c988ab0db6d1db34e97f066b94938568c1a8.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/_geometry.cpython-312-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/f8 objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/_geometry.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/f8/77d9860c21166a22eec008955f9ca0b7d4ce3d.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/f8/77d9860c21166a22eec008955f9ca0b7d4ce3d.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/_geometry.cpython-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/f8/77d9860c21166a22eec008955f9ca0b7d4ce3d.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/_geometry.cpython-311-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/f0 objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighbors.cpython-312-aarch64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/f0/1d93a729b6d43193046b3d6b028feb3d990338.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/f0/1d93a729b6d43193046b3d6b028feb3d990338.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighbors.cpython-312-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/f0/1d93a729b6d43193046b3d6b028feb3d990338.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighbors.cpython-312-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/c9 objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighbors.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/c9/7b552459cd16b56e9042058ffa723766813bdc.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/c9/7b552459cd16b56e9042058ffa723766813bdc.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighbors.cpython-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/c9/7b552459cd16b56e9042058ffa723766813bdc.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighbors.cpython-311-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/35 objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighborlist.cpython-312-aarch64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/35/5eccdb467071d3deb3d5e063a0064a449ab2cb.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/35/5eccdb467071d3deb3d5e063a0064a449ab2cb.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighborlist.cpython-312-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/35/5eccdb467071d3deb3d5e063a0064a449ab2cb.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighborlist.cpython-312-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/35 objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighborlist.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/35/6683d38c20cb805018eff2fe9845a1d0888da4.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/35/6683d38c20cb805018eff2fe9845a1d0888da4.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighborlist.cpython-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/35/6683d38c20cb805018eff2fe9845a1d0888da4.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighborlist.cpython-311-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/d1 objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/drid.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/d1/754df5ae942527b8017f14f757095d43eefe75.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/d1/754df5ae942527b8017f14f757095d43eefe75.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/drid.cpython-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/d1/754df5ae942527b8017f14f757095d43eefe75.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/drid.cpython-311-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/91 objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/drid.cpython-312-aarch64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/91/3b15b0c2fd7b1ebd04884d07a18da86add6167.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/91/3b15b0c2fd7b1ebd04884d07a18da86add6167.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/drid.cpython-312-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/91/3b15b0c2fd7b1ebd04884d07a18da86add6167.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/drid.cpython-312-aarch64-linux-gnu.so strip --strip-debug --remove-section=.comment --remove-section=.note --enable-deterministic-archives -R .gnu.lto_\* -R .gnu.debuglto_\* -N __gnu_lto_slim -N __gnu_lto_v1 debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/core/lib/libtheobald.a install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.dwz cp --reflink=auto -a debian/python3-mdtraj/usr/lib/debug/.dwz/aarch64-linux-gnu debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.dwz rm -fr debian/python3-mdtraj/usr/lib/debug/.dwz rmdir -p --ignore-fail-on-non-empty debian/python3-mdtraj/usr/lib/debug install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/share/doc ln -s python3-mdtraj debian/.debhelper/python3-mdtraj/dbgsym-root/usr/share/doc/python3-mdtraj-dbgsym install -m0755 -d debian/.debhelper/python3-mdtraj dh_makeshlibs -a -O--buildsystem=pybuild rm -f debian/python3-mdtraj/DEBIAN/shlibs dh_shlibdeps -a -O--buildsystem=pybuild install -m0755 -d debian/python3-mdtraj/DEBIAN dpkg-shlibdeps -Tdebian/python3-mdtraj.substvars debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_rmsd.cpython-312-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_rmsd.cpython-311-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_lprmsd.cpython-312-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_lprmsd.cpython-311-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dtr.cpython-312-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/xtc.cpython-312-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/xtc.cpython-311-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/tng.cpython-311-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/tng.cpython-312-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dtr.cpython-311-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/trr.cpython-312-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/trr.cpython-311-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dcd.cpython-311-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dcd.cpython-312-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/binpos.cpython-312-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/binpos.cpython-311-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/_geometry.cpython-312-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/_geometry.cpython-311-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighbors.cpython-312-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighbors.cpython-311-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighborlist.cpython-312-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighborlist.cpython-311-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/drid.cpython-311-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/drid.cpython-312-aarch64-linux-gnu.so dh_installdeb -O--buildsystem=pybuild install -m0755 -d debian/python3-mdtraj/DEBIAN printf '#!/bin/sh\nset -e\n' > debian/python3-mdtraj/DEBIAN/postinst cat debian/python3-mdtraj.postinst.debhelper >> debian/python3-mdtraj/DEBIAN/postinst chmod 0755 -- debian/python3-mdtraj/DEBIAN/postinst printf '#!/bin/sh\nset -e\n' > debian/python3-mdtraj/DEBIAN/prerm cat debian/python3-mdtraj.prerm.debhelper >> debian/python3-mdtraj/DEBIAN/prerm chmod 0755 -- debian/python3-mdtraj/DEBIAN/prerm install -m0755 -d debian/python-mdtraj-doc/DEBIAN dh_gencontrol -O--buildsystem=pybuild install -m0755 -d debian/python-mdtraj-doc/DEBIAN echo misc:Depends= >> debian/python-mdtraj-doc.substvars echo misc:Pre-Depends= >> debian/python-mdtraj-doc.substvars dpkg-gencontrol -ppython-mdtraj-doc -ldebian/changelog -Tdebian/python-mdtraj-doc.substvars -cdebian/control -Pdebian/python-mdtraj-doc install -m0755 -d debian/python3-mdtraj/DEBIAN echo misc:Depends= >> debian/python3-mdtraj.substvars echo misc:Pre-Depends= >> debian/python3-mdtraj.substvars install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/DEBIAN dpkg-gencontrol -ppython3-mdtraj -ldebian/changelog -Tdebian/python3-mdtraj.substvars -cdebian/control -Pdebian/.debhelper/python3-mdtraj/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -UProtected -UBuilt-Using -UStatic-Built-Using -DPackage=python3-mdtraj-dbgsym "-DDepends=python3-mdtraj (= \${binary:Version})" "-DDescription=debug symbols for python3-mdtraj" "-DBuild-Ids=0649067756663be460c738d4e8284ea0ecd87375 25ec669c9693bdda7b7b2869026df91dbf75fb27 2828dc983153d150fc070173a098386362d964c4 2f0bc8f8923e8272f7723445cada8ab49413817a 30a547a8931b707ad5e76d427c7be844910f17e2 355eccdb467071d3deb3d5e063a0064a449ab2cb 356683d38c20cb805018eff2fe9845a1d0888da4 364fe6512e3f023d8c9b3688037312c48d6e4820 499b3b1aedc1aced6a292c1006726a66ad9f1e06 6a3205ed0388d44b4c1e2ad7d4e7e1e9d41ace84 6e7df4bccb447cef575158ccd534c5564fa8a273 716ddafa19c853611670dcfecda6efbec3e6bbff 735aa1afe088160437b05ee8c737be6107b020fe 913b15b0c2fd7b1ebd04884d07a18da86add6167 b2ce5bb391bff5ea7af7c4a8e65deae8b40a136e c97b552459cd16b56e9042058ffa723766813bdc cd5f0de02111520c5fb18a88ed2822fc2d08e571 d088c988ab0db6d1db34e97f066b94938568c1a8 d1754df5ae942527b8017f14f757095d43eefe75 ddc1a6f731b4ff4e0e89198c0405fb943c207ffe dfe184c717f6d8ae87fc563bb6589c4c85cf6578 f01d93a729b6d43193046b3d6b028feb3d990338 f6d9895d1c7c2f3d41a8259129d34863a1848ad3 f877d9860c21166a22eec008955f9ca0b7d4ce3d" -DSection=debug -UMulti-Arch -UReplaces -UBreaks dpkg-gencontrol: warning: package python-mdtraj-doc: substitution variable ${python3:Depends} unused, but is defined dpkg-gencontrol: warning: package python-mdtraj-doc: substitution variable ${sphinxdoc:Built-Using} unused, but is defined chmod 0644 -- debian/python-mdtraj-doc/DEBIAN/control chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/DEBIAN/control dpkg-gencontrol -ppython3-mdtraj -ldebian/changelog -Tdebian/python3-mdtraj.substvars -cdebian/control -Pdebian/python3-mdtraj chmod 0644 -- debian/python3-mdtraj/DEBIAN/control dh_md5sums -O--buildsystem=pybuild install -m0755 -d debian/python3-mdtraj/DEBIAN cd debian/python3-mdtraj >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums install -m0755 -d debian/python-mdtraj-doc/DEBIAN cd debian/python-mdtraj-doc >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/python3-mdtraj/DEBIAN/md5sums install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/DEBIAN cd debian/.debhelper/python3-mdtraj/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/python-mdtraj-doc/DEBIAN/md5sums chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/DEBIAN/md5sums dh_builddeb -O--buildsystem=pybuild dpkg-deb --root-owner-group --build debian/python3-mdtraj .. dpkg-deb --root-owner-group --build debian/.debhelper/python3-mdtraj/dbgsym-root .. dpkg-deb: building package 'python3-mdtraj' in '../python3-mdtraj_1.9.9-1_arm64.deb'. dpkg-deb: building package 'python3-mdtraj-dbgsym' in '../python3-mdtraj-dbgsym_1.9.9-1_arm64.deb'. dpkg-deb --root-owner-group --build debian/python-mdtraj-doc .. dpkg-deb: building package 'python-mdtraj-doc' in '../python-mdtraj-doc_1.9.9-1_all.deb'. dpkg-genbuildinfo --build=binary -O../mdtraj_1.9.9-1_arm64.buildinfo dpkg-genchanges --build=binary -O../mdtraj_1.9.9-1_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-source: info: using options from mdtraj-1.9.9/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/4115798/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/4115798/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/4115798 and its subdirectories I: Current time: Fri May 3 04:24:40 +14 2024 I: pbuilder-time-stamp: 1714659880